From 89899a27bb5a4436f55f1d84a5f0d25cbda47dff Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Fri, 9 Jan 2026 20:39:17 -0500 Subject: [PATCH 1/9] integrate templateflow --- ...ce-ICBM2009sym_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...l-Agile12v2016_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...I152Lin_res-01_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...009bAsym_res-1_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...2009bSym_res-1_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...09cAsym_res-01_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...2009cSym_res-1_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...in6Asym_res-01_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...Lin6Sym_res-01_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ .../tpl-MNI305_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...tpl-MNIColin27_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...S30ANTs_res-01_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...pl-PD25-res-01_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ ...res-01_den-41k_desc-groundtruth_afids.fcsv | 35 +++++++++++++++++++ 14 files changed, 490 insertions(+) create mode 100644 autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI152NLin6Sym_res-01_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv create mode 100644 autoafids/resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv diff --git a/autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..888e7e7 --- /dev/null +++ b/autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,0.265,2.6205,-4.1925,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.1965,-25.3475,-2.4835,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.4325,-39.0585,-16.3025,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.465,-22.9715,-21.68,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.1885,-12.8125,-10.9745,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,12.7105,-27.041,-10.1395,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-12.4665,-27.064,-10.7585,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,10.599,-30.311,-22.488,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.1095,-30.4125,-23.7145,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.181,-43.383,4.344,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.1555,-7.959,-14.9365,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.513,-7.9635,-13.463,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.853,-8.271,-13.936,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.2725,-34.4745,3.558,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,16.213,4.4325,25.801,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-16.143,4.4655,25.685,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,19.58,-23.463,28.507,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-19.666,-23.452,27.885,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.025,33.2105,3.1305,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.563,-39.4115,7.6585,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.341,-4.7005,-26.1515,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-33.368,-5.6025,-22.4175,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,17.6445,-10.098,-18.0085,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-18.851,-9.6085,-19.1485,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,20.57,-5.055,-27.248,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-19.613,-5.212,-26.086,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,12.5145,-43.3165,6.002,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-13.21,-43.0065,6.5705,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,19.5905,-83.6925,3.927,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-18.1015,-84.7275,-0.1355,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.4725,20.1715,-11.854,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.385,20.7985,-11.4635,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..a092607 --- /dev/null +++ b/autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,4.1493909375,5.678821875,1.4795320625,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,3.230568125,-19.9064125,-4.8756628125,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,2.7960728125,-28.60988125,-16.037834375,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,3.421190625,-13.23296875,-20.471746875,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,3.7356490625,-7.0098490625,-8.73979625,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,15.00718125,-18.92895,-11.42105,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-8.9887453125,-18.22670625,-11.611440625,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,12.9510625,-19.957878125,-22.0481875,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-6.58012,-18.918334375,-21.962928125,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,1.9017196875,-45.484784375,-8.999916875,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,4.1233628125,-0.9788696875,-10.8898759375,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,6.2728634375,-1.11923546875,-10.12487625,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,2.0539009375,-1.0529093125,-10.1125115625,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,2.7084884375,-25.85953125,-4.796835625,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,18.588353125,-1.43555084375,27.09186875,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-10.36823125,-0.48472604996875,26.8761625,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,19.9445125,-27.044696875,20.790275,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-14.211640625,-25.8343,20.192028125,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,5.6998965625,30.37541875,17.899746875,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,2.7595959375,-33.2157875,-1.4735090625,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.593409375,4.67608296875,-19.13281875,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-26.09055,5.6104065625,-18.54696875,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,20.01790625,-2.7720371875,-12.648403125,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-12.713090625,-1.5686535,-13.346115625,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,23.83704375,5.44529328125,-20.423478125,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-15.429971875,6.27710625,-20.405490625,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,15.39044375,-36.3536625,-4.7835621875,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-11.80639375,-36.848665625,-5.417424375,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,17.988434375,-72.19396875,-15.9282,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-17.312128125,-72.209359375,-16.6732875,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,16.650659375,21.919425,1.23355321875,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-6.7836909375,22.16438125,-0.05127345,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..dbfd695 --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,0.265,2.8417499999999998,-4.8774999999999995,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.2445,-27.409750000000003,-3.4354999999999998,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.4515,-37.737750000000005,-11.50975,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.44575,-22.92625,-20.76375,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.3135,-16.02675,-12.569500000000001,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,12.102500000000001,-27.875,-11.502500000000001,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-10.94475,-28.10075,-11.72175,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,11.13075,-30.933750000000003,-20.5895,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.21625,-31.3505,-21.23725,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.38425,-53.887499999999996,1.59275,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,0.452,-8.468,-14.756499999999999,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.9812499999999997,-8.50625,-14.4335,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-1.8632499999999999,-8.5285,-14.462,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.446,-32.061,-0.18025,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.64825,3.7824999999999998,24.4835,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-14.961,3.7824999999999998,24.49425,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,20.096,-27.11825,25.02375,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-19.12425,-27.432,25.043499999999998,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.27575,33.002,3.20125,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.389,-38.60775,5.9295,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,35.3565,-5.468999999999999,-24.86,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-33.27625,-8.8255,-23.63625,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,21.103749999999998,-10.334999999999999,-17.2245,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-18.887500000000003,-11.908750000000001,-16.926750000000002,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,21.724999999999998,-4.606,-28.0105,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-19.297,-5.2415,-25.759500000000003,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,14.356499999999999,-38.446,3.676,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-14.013,-40.19825,2.217,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,21.1005,-78.59375,3.8802499999999993,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-18.045499999999997,-82.6635,2.4375,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.953,17.591749999999998,-12.82825,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.935749999999999,17.182249999999996,-13.61225,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..4ef3056 --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-0.204861407692308,2.72288076923077,-4.88105282051282,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,-0.00726026948717949,-25.0450538461538,-2.21068230769231,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.025998141025641,-37.691917948718,-11.0111497435897,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,-0.0892198512820513,-23.1885743589744,-21.5288358974359,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,-0.05649251,-13.7676564102564,-10.950028974359,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.3113025641026,-25.951058974359,-9.74885435897436,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-13.607458974359,-26.4451,-9.7076082051282,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,10.8321820512821,-30.8104076923077,-21.5949358974359,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.9824102564103,-30.8778025641026,-21.4372025641026,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.0100564897435897,-52.5094615384615,2.14842435897436,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.0743417574102564,-8.36030051282051,-15.9354820512821,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.02761256410256,-8.15453153846154,-15.0245538461538,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.19342487179487,-8.21593282051282,-15.0426743589744,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.00940744421052632,-31.5985789473684,0.568596455263158,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.1850526315789,5.61940868421053,24.9488552631579,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-15.7984342105263,5.47038342105263,25.0905473684211,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,18.7231289473684,-22.0626210526316,28.0333394736842,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.4848157894737,-22.2426736842105,28.1745157894737,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,-0.111086676315789,33.3615236842105,2.12355523157895,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.116840065,-37.6019447368421,6.49650894736842,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.0034921052632,-4.056905,-27.3505,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-34.8327763157895,-6.646575,-25.3468578947368,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,17.4263131578947,-10.0524047368421,-18.2650921052632,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-18.1468184210526,-10.9803721052632,-18.3750131578947,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,20.4641447368421,-4.03479921052632,-28.0214973684211,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-21.3443842105263,-5.12460973684211,-27.9912052631579,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,14.6365184210526,-40.7174131578947,4.71004973684211,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-14.8907842105263,-43.0901605263158,4.23491921052632,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.8308868421053,-79.2528368421053,4.51120236842105,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-18.9085052631579,-82.82955,3.54751710526316,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,11.8931421052632,18.5102315789474,-12.3773210526316,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-13.3650815789474,17.0294973684211,-13.0638105263158,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..3b9d48e --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-0.1198055,2.55212,-4.81723,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.1409195,-25.124,-2.096035,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.130151,-37.8742,-10.05817,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.0267405,-23.35095,-21.87635,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,-0.01609995,-14.39165,-10.7025,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.3752,-26.0718,-9.788495,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-13.05015,-26.38415,-9.760085,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,11.1066,-30.21855,-21.3211,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.8376,-30.35535,-21.02715,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,-0.0609305,-52.3597,2.02387,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.175911,-8.20253,-15.39965,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.10252,-8.12621,-14.502,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-1.850385,-7.991405,-14.413,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,-0.183038,-31.2358,0.586406,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.1932,6.031435,25.2426,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-15.43225,6.228585,24.9267,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,18.54945,-22.73095,28.598,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.6767,-22.7815,28.42485,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.002431,33.43875,2.52457,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.132994,-37.6245,6.401015,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.47875,-4.880005,-26.81425,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-34.3701,-4.84792,-26.9405,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,17.93685,-10.93965,-17.9412,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-18.21465,-10.78475,-18.1403,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,20.91065,-4.410115,-27.6511,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-20.9084,-4.5878,-27.29665,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,13.69415,-43.103,5.85519,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-13.33945,-43.3071,5.90314,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,19.8371,-81.1685,3.90738,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-19.93535,-81.2627,4.248705,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.54255,17.7086,-12.74795,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.8065,18.11375,-12.85975,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..e533f27 --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-0.204861407692308,2.72288076923077,-4.88105282051282,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,-0.00726026948717949,-25.0450538461538,-2.21068230769231,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.025998141025641,-37.691917948718,-11.0111497435897,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,-0.0892198512820513,-23.1885743589744,-21.5288358974359,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,-0.05649251,-13.7676564102564,-10.950028974359,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.3113025641026,-25.951058974359,-9.74885435897436,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-13.607458974359,-26.4451,-9.7076082051282,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,10.8321820512821,-30.8104076923077,-21.5949358974359,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.9824102564103,-30.8778025641026,-21.4372025641026,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.0100564897435897,-52.5094615384615,2.14842435897436,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.0743417574102564,-8.36030051282051,-15.9354820512821,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.02761256410256,-8.15453153846154,-15.0245538461538,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.19342487179487,-8.21593282051282,-15.0426743589744,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.00940744421052632,-31.5985789473684,0.568596455263158,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.1850526315789,5.61940868421053,24.9488552631579,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-15.7984342105263,5.47038342105263,25.0905473684211,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,18.7231289473684,-22.0626210526316,28.0333394736842,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.4848157894737,-22.2426736842105,28.1745157894737,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,-0.111086676315789,33.3615236842105,2.12355523157895,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.116840065,-37.6019447368421,6.49650894736842,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.0034921052632,-4.056905,-27.3505,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-34.8327763157895,-6.646575,-25.3468578947368,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,17.4263131578947,-10.0524047368421,-18.2650921052632,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-18.1468184210526,-10.9803721052632,-18.3750131578947,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,20.4641447368421,-4.03479921052632,-28.0214973684211,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-21.3443842105263,-5.12460973684211,-27.9912052631579,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,14.6365184210526,-40.7174131578947,4.71004973684211,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-14.8907842105263,-43.0901605263158,4.23491921052632,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.5600675675676,-79.8774891891892,4.60286108108108,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-18.9085052631579,-82.82955,3.54751710526316,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,11.8931421052632,18.5102315789474,-12.3773210526316,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-13.3650815789474,17.0294973684211,-13.0638105263158,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 \ No newline at end of file diff --git a/autoafids/resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..a7eff1f --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-0.06725,2.8625,-4.833,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,-0.08449999999999999,-25.1645,-1.935,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,-0.036750000000000005,-37.904999999999994,-12.25175,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.092,-23.63375,-21.429,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,-0.01375,-13.621,-11.32725,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.12325,-26.3525,-9.777000000000001,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-13.6855,-26.3955,-9.554,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,11.1195,-30.851,-21.99175,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-11.11475,-30.957749999999997,-22.075,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,-0.2355,-52.72925,1.9145,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.013999999999999995,-8.295,-16.229,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.232,-8.0815,-14.92775,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.2039999999999997,-8.10775,-14.858,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,-0.05125,-31.646250000000002,0.44525000000000003,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.315000000000001,5.22375,24.67375,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-15.31825,5.2265,24.732,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,18.7605,-22.9955,27.704250000000002,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.75525,-22.926,27.444999999999997,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.12949999999999998,33.259,1.9165,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,-0.18475,-37.6545,6.0825,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.238249999999994,-5.7415,-26.74375,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-34.24725,-6.14975,-26.351999999999997,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,18.3745,-10.984,-17.58725,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-18.55675,-11.1765,-17.7785,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,21.77375,-4.7692499999999995,-29.44175,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-22.153000000000002,-4.979500000000001,-29.33125,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,14.4425,-42.2705,4.43325,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-14.478,-42.569750000000006,4.25425,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.255000000000003,-80.53275000000001,4.89525,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-19.86775,-81.0495,4.46075,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.474250000000001,16.982499999999998,-13.2695,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.88525,17.2745,-13.21375,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..bcc0a43 --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,0.402,2.5665,-5.312750000000001,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.52625,-25.466749999999998,-2.261,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.38675,-37.50125,-11.652999999999999,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.5599999999999999,-23.65125,-20.8645,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.4795,-14.091,-11.051000000000002,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,12.589,-27.009999999999998,-10.4315,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-11.97875,-27.383499999999998,-10.471,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,11.096749999999998,-31.156,-21.80775,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.125499999999999,-31.092000000000002,-21.546,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.25975000000000004,-52.1315,1.31175,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,0.48000000000000004,-8.59625,-15.615749999999998,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.6864999999999997,-8.45,-14.895,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-1.8592500000000003,-8.43425,-14.847999999999999,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.53725,-31.66475,0.3555,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.08925,5.01025,23.69375,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-14.49275,5.0352500000000004,23.57325,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,19.29225,-23.075,26.0725,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.10325,-23.107000000000003,26.18325,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.5052500000000001,32.68625,3.147,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.62675,-37.77625,5.970000000000001,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,35.108000000000004,-5.78625,-25.394,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-32.951499999999996,-7.51,-24.64675,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,18.68825,-10.3385,-17.303,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-17.9405,-11.03625,-17.4545,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,21.373250000000002,-4.13075,-26.94975,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-21.49075,-4.686999999999999,-27.414,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,14.418750000000001,-41.43375,4.6135,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-13.224499999999999,-42.499750000000006,4.051,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,21.46,-78.0805,3.601,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-18.810250000000003,-80.85549999999999,3.2502500000000003,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.72325,17.876,-12.12775,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.652000000000001,17.16875,-12.67675,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152NLin6Sym_res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin6Sym_res-01_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..8ff1d4a --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI152NLin6Sym_res-01_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-0.002749999999999999,2.5065,-4.1025,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,-0.013499999999999998,-25.246000000000002,-2.14525,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,-0.043250000000000004,-37.381,-11.91,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,-0.045,-23.987750000000002,-21.08325,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,-0.018250000000000002,-13.46425,-10.9435,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,12.65625,-26.993000000000002,-9.847750000000001,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-12.9745,-26.796750000000003,-9.88975,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,10.881499999999999,-31.073499999999996,-21.94925,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.83325,-31.1095,-21.926000000000002,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.0055,-53.562999999999995,2.02025,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.06275,-8.10725,-15.47,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.23475,-8.14125,-14.59975,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.4762500000000003,-8.14725,-14.62125,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,-0.06025,-31.80925,1.04025,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.232,4.07225,24.734,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-15.204749999999999,4.044,24.799,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,18.6545,-23.72525,26.94025,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.4735,-23.73575,27.1125,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,-0.0485,33.619,2.9905,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,-0.04575,-37.903,6.6392500000000005,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.1785,-6.751,-25.7565,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-34.300250000000005,-6.83225,-25.673750000000002,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,19.13525,-10.780249999999999,-16.93425,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-19.17075,-10.82125,-16.899250000000002,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,21.55525,-5.1635,-27.14675,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-21.43575,-4.77325,-27.136000000000003,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,13.57075,-42.54575,5.10075,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-14.163999999999998,-42.568250000000006,5.109,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.907000000000004,-78.422,5.17825,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-20.80825,-78.37125,5.078250000000001,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.6275,18.14575,-12.206,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.64125,17.96375,-12.3105,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..2dcaa26 --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.10 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,0.38425000000000004,1.63575,-4.784,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.2745,-29.36975,-4.03825,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.20650000000000004,-38.08225,-12.4535,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.62325,-23.0955,-20.8555,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.31675000000000003,-15.37825,-10.81575,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.186250000000001,-28.18875,-11.696,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-11.645,-28.647750000000002,-11.3545,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,11.25525,-32.765,-22.72525,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-9.597,-33.005250000000004,-23.125,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,-0.12175000000000001,-51.568,0.9937499999999998,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,0.45000000000000007,-9.932500000000001,-15.17975,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.73975,-9.79425,-15.22175,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.19525,-9.47325,-15.28475,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.43125,-35.63275,-0.52875,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,14.181000000000001,2.50225,23.698500000000003,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-14.02875,2.58875,23.88675,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,19.826499999999996,-28.7645,24.676,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.39825,-28.641,24.98875,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.03925,31.401500000000002,5.4685,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.525,-39.41825,5.409000000000001,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,36.10575,-10.73675,-23.56175,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-33.93725,-10.72275,-23.552,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,22.42975,-10.911000000000001,-18.08475,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-22.23925,-12.456750000000001,-18.784,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,28.859250000000003,-8.495,-25.996499999999997,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-28.120250000000002,-9.931249999999999,-24.659750000000003,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,16.698,-40.57575,0.10724999999999996,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-15.8635,-41.180499999999995,-1.15375,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.802,-78.6385,3.22525,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-19.452749999999998,-80.11975,2.7747499999999996,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,12.02425,14.88375,-12.5785,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-13.2365,14.7675,-12.539750000000002,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..df87509 --- /dev/null +++ b/autoafids/resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,0.547527528125,4.007721875,-5.85731125,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.31921995625,-23.23456875,-3.72751125,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.561583,-34.45210625,-12.8559625,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.6079103125,-19.538690625,-21.89735,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.4886344625,-11.1283246875,-11.5526875,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,14.08818125,-23.66650625,-11.0875246875,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-12.717509375,-24.440084375,-10.993478125,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,12.1797375,-27.100284375,-22.624340625,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-11.1640475,-27.94559375,-22.2905875,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.665826690625,-52.2055875,4.512423125,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,0.9424654375,-5.88735375,-16.407625,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,3.49182,-5.5838253125,-15.65260625,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-1.44826446875,-5.720745,-15.537396875,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.1166158878125,-28.649928125,-0.33771765625,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,15.011765625,6.1724759375,22.566596875,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-15.90715,6.4662878125,24.069828125,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,17.972071875,-20.823715625,30.46349375,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.779996875,-20.611896875,30.416096875,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.70195960625,35.429990625,1.760076875,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.108530173125,-32.37980625,10.1816840625,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,36.0364625,-1.0992918125,-29.31504375,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-33.24596875,-2.996340625,-27.734278125,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,19.775496875,-7.527871875,-17.524228125,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-19.331309375,-8.076225625,-18.7995,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,23.89074375,-1.8913829375,-27.64306875,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-20.382253125,-3.704695625,-28.9971,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,13.6410125,-38.46600625,8.433885625,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-14.791465625,-40.95736875,8.190668125,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,27.4747875,-63.9652125,2.0995312825,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-23.890625,-69.7058125,2.33407990625,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,13.3516125,22.4382375,-11.7592125,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-13.322734375,21.3597625,-12.51313125,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..8ccb65d --- /dev/null +++ b/autoafids/resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-109.9665,-134.07325,-129.8755,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,-110.03925000000001,-160.93525,-129.458,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,-109.98349999999999,-172.01975000000002,-140.20274999999998,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,-110.0005,-158.62125,-146.06799999999998,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,-110.00875,-149.2665,-136.6645,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,-98.47075,-161.65225,-136.55675,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-121.717,-161.79000000000002,-136.67625,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,-100.04124999999999,-164.08325,-146.678,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-119.78,-164.05975,-146.71425,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,-110.39375,-187.82275,-129.085,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-109.80949999999999,-143.49375,-140.37925,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,-107.64874999999999,-143.5275,-139.6105,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-111.99875,-143.52799999999996,-139.65800000000002,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,-110.194,-166.5135,-127.24999999999999,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,-95.38300000000001,-133.7965,-104.49575,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-124.41499999999999,-133.75725,-104.61949999999999,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,-92.27824999999999,-160.54449999999997,-104.01150000000001,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-127.8655,-160.422,-104.15650000000001,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,-109.97075000000001,-105.47575,-120.11574999999999,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,-109.95825,-172.67475000000002,-123.883,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,-78.09025,-139.83325,-149.31799999999998,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-141.27375,-140.64800000000002,-148.89875,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,-91.79324999999999,-145.865,-141.126,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-128.36450000000002,-146.24775,-141.16375,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,-89.50150000000001,-138.7625,-150.98025,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-129.80775,-139.208,-151.2225,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,-97.061,-176.29500000000002,-125.12225,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-124.50725,-177.8245,-126.14250000000001,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,-91.17325000000001,-211.98725,-127.92825,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-128.1335,-214.29475,-128.61875,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,-98.2075,-118.40350000000001,-135.2765,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-121.63900000000001,-118.67850000000001,-135.93175,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..bf21410 --- /dev/null +++ b/autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.10 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,-0.23650000000000002,3.362,-3.64,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,-0.181,-25.177,-1.0295,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,-0.051,-36.6575,-9.397,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,-0.147,-23.484499999999997,-19.863500000000002,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.0,-14.456,-9.4235,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.243500000000001,-25.8875,-8.621500000000001,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-13.995000000000001,-26.308999999999997,-8.4855,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,10.722,-31.064,-19.9825,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-11.2515,-30.956000000000003,-19.9625,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,-0.362,-52.185500000000005,2.6505,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,-0.1765,-7.6645,-13.91,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,2.0845000000000002,-8.0915,-12.946,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-2.621,-7.977499999999999,-12.905000000000001,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,-0.4595,-32.0995,1.825,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,16.070999999999998,7.5855,25.072499999999998,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-16.5295,7.5005,25.117,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,18.744,-24.8485,29.307499999999997,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-18.878,-25.000500000000002,28.9835,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,-0.021500000000000005,34.516999999999996,1.5135,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,-0.118,-37.42,8.0315,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,34.439499999999995,-4.3065,-26.737000000000002,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-35.7425,-7.0745000000000005,-25.0885,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,18.9895,-10.061499999999999,-16.5675,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-20.787,-11.126,-16.436,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,21.685,-4.7955000000000005,-29.0085,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-23.0095,-5.751,-28.208,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,16.473,-41.2255,4.532500000000001,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-15.3925,-43.3945,4.894500000000001,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.567999999999998,-77.83099999999999,5.7245,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-19.775,-80.1425,6.2545,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,11.855,19.5445,-13.033000000000001,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-13.587499999999999,17.979,-13.321,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv new file mode 100644 index 0000000..a54f1e9 --- /dev/null +++ b/autoafids/resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv @@ -0,0 +1,35 @@ +# Markups fiducial file version = 4.6 +# CoordinateSystem = 0 +# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID +vtkMRMLMarkupsFiducialNode_1,0.658,1.6740000000000002,-6.0504999999999995,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_2,0.48325,-26.781,-3.0147500000000003,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_3,0.49274999999999997,-38.945750000000004,-11.130999999999998,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_4,0.68575,-24.37825,-20.09825,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_5,0.70275,-15.460249999999998,-10.07575,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_6,13.05875,-28.90575,-9.8035,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_7,-12.185749999999999,-28.46,-10.2395,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_8,12.1425,-32.0705,-21.53,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_9,-10.5765,-31.889499999999998,-22.0805,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_10,0.4139999999999999,-53.025499999999994,-1.3547500000000001,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_11,0.618,-10.39525,-13.24025,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_12,3.18625,-10.0345,-13.102,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_13,-1.94475,-10.212,-13.86825,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_14,0.48974999999999996,-32.17725,0.54075,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_15,18.40075,2.3815,27.63075,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_16,-17.39975,3.1940000000000004,27.208750000000002,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_17,20.4895,-26.69025,27.59325,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_18,-19.8915,-25.717,27.66325,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_19,0.5635,34.322500000000005,2.86925,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_20,0.37174999999999997,-39.53175,4.87925,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_21,35.148250000000004,-7.5575,-26.124,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_22,-33.030249999999995,-7.855750000000001,-26.443250000000003,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_23,23.073999999999998,-11.91725,-16.86825,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_24,-22.32175,-12.18125,-16.9795,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_25,24.83325,-6.15925,-26.667499999999997,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_26,-23.9145,-5.99275,-26.131,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_27,14.036500000000002,-40.566,2.32275,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_28,-13.159,-40.59325,1.8685,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_29,20.364250000000002,-81.697,3.2545,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_30,-19.13375,-82.56475,2.3285,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_31,13.18975,16.3695,-13.29825,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 +vtkMRMLMarkupsFiducialNode_32,-12.841249999999999,15.933,-14.65,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 From 95abdde0df7a8fa88954a9bb9edeae90169d7215 Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Sun, 11 Jan 2026 15:05:30 -0500 Subject: [PATCH 2/9] add logic --- autoafids/config/snakebids.yml | 7 +++ autoafids/workflow/envs/templateflow.yaml | 4 ++ autoafids/workflow/rules/regqc.smk | 55 ++++++++++++++++++---- autoafids/workflow/scripts/templateflow.py | 9 ++++ 4 files changed, 66 insertions(+), 9 deletions(-) create mode 100644 autoafids/workflow/envs/templateflow.yaml create mode 100644 autoafids/workflow/scripts/templateflow.py diff --git a/autoafids/config/snakebids.yml b/autoafids/config/snakebids.yml index 0f38839..b28eb59 100644 --- a/autoafids/config/snakebids.yml +++ b/autoafids/config/snakebids.yml @@ -147,6 +147,13 @@ parse_args: default: false required: false + --template-flow: + help: 'Downloads a template from templateflow and uses it to assess the quality of registration.' + choices: ['Agile12v2016', 'MNI152Lin ', 'MNI152NLin2009cAsym', 'MNI152NLin6Sym', 'OASIS30ANTs', 'BigBrainSym' , 'MNI152NLin2009bAsym', 'MNI152NLin2009cSym', 'MNI305', 'PD25', 'fsaverage', 'MNI152NLin2009bSym', 'MNI152NLin6Asym','MNIColin27'] + default: false + required: false + type: str + --fidqc: help: 'Generate *.html files for QC of AutoAFIDs outputs. (default: %(default)s)' dest: "fidqc" diff --git a/autoafids/workflow/envs/templateflow.yaml b/autoafids/workflow/envs/templateflow.yaml new file mode 100644 index 0000000..e8ca27d --- /dev/null +++ b/autoafids/workflow/envs/templateflow.yaml @@ -0,0 +1,4 @@ +--- +name: templateflow +channels: [conda-forge, defaults] +dependencies: [python=3.9, templateflow] \ No newline at end of file diff --git a/autoafids/workflow/rules/regqc.smk b/autoafids/workflow/rules/regqc.smk index aecee5e..84c67fe 100644 --- a/autoafids/workflow/rules/regqc.smk +++ b/autoafids/workflow/rules/regqc.smk @@ -4,6 +4,25 @@ import glob lead_dbs_dir = config.get("LEAD_DBS_DIR", False) fmriprep_dir = config.get("FMRIPREP_DIR", False) +template_name = config.get("template_flow", '') + +template_dict = { + "Agile12v2016" : 'resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv', + "MNI152Lin" : 'resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv', + "MNI152NLin2009cAsym" : 'resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv', + "MNI152NLin6Sym" : 'resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv', + "OASIS30ANTs" : 'resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv', + "BigBrainSym" : 'resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv', + "MNI152NLin2009bAsym" : 'resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv', + "MNI152NLin2009cSym" : 'resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv', + "MNI305" : 'resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv', + "PD25" : 'resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv', + "fsaverage" : 'resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv', + "MNI152NLin2009bSym" : 'resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv', + "MNI152NLin6Asym" : 'resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv', + "MNIColin27" : 'resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv', +} + def get_warp_path(subject): if lead_dbs_dir: @@ -89,18 +108,36 @@ def get_resampled_im(subject): def get_ref_paths(): - if lead_dbs_dir: - refimage = str( - Path(workflow.basedir).parent / config["templatet1w_lead"] - ) - refcoordinate = str( - Path(workflow.basedir).parent / config["fcsv_mni_lead"] - ) + if template_name: + refimage=directory(Path(download_dir) / "templateflow" / template_name) + refcoordinate=template_dict[template_name] else: - refimage = str(Path(workflow.basedir).parent / config["templatet1w"]) - refcoordinate = str(Path(workflow.basedir).parent / config["fcsv_mni"]) + if lead_dbs_dir: + refimage = str( + Path(workflow.basedir).parent / config["templatet1w_lead"] + ) + refcoordinate = str( + Path(workflow.basedir).parent / config["fcsv_mni_lead"] + ) + else: + refimage = str(Path(workflow.basedir).parent / config["templatet1w"]) + refcoordinate = str(Path(workflow.basedir).parent / config["fcsv_mni"]) return refimage, refcoordinate +rule download_template: + params: + template=template_name, + output: + template_dir=directory(Path(download_dir) / "templateflow"), + log: + bids( + root="logs", + suffix="downlaod_template.log", + ), + conda: + "../envs/templateflow.yaml" + script: + "../scripts/templateflow.py" rule regqc: input: diff --git a/autoafids/workflow/scripts/templateflow.py b/autoafids/workflow/scripts/templateflow.py new file mode 100644 index 0000000..6bcb0aa --- /dev/null +++ b/autoafids/workflow/scripts/templateflow.py @@ -0,0 +1,9 @@ +import os +from templateflow import api as tflow + +template_name = snakemake.params["template"] +output_dir = snakemake.output["template_dir"] + +os.environ['TEMPLATEFLOW_HOME'] = output_dir + +tflow.get(template_name, desc=None, resolution=1, suffix='T1w', extension='nii.gz') \ No newline at end of file From 7b0cb7ee9ced94dbad84f6ecf4713daf0ad8c40f Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Tue, 13 Jan 2026 13:03:38 -0500 Subject: [PATCH 3/9] debug the logic to synchronize download_template rule with regqc feature --- autoafids/run.py | 3 +++ autoafids/workflow/rules/cnn.smk | 4 ++-- autoafids/workflow/rules/regqc.smk | 21 ++++++++++----------- autoafids/workflow/scripts/regqc.py | 10 +++++++--- autoafids/workflow/scripts/template_flow.py | 5 +++++ autoafids/workflow/scripts/templateflow.py | 9 --------- 6 files changed, 27 insertions(+), 25 deletions(-) create mode 100644 autoafids/workflow/scripts/template_flow.py delete mode 100644 autoafids/workflow/scripts/templateflow.py diff --git a/autoafids/run.py b/autoafids/run.py index 4f7b033..94a058c 100755 --- a/autoafids/run.py +++ b/autoafids/run.py @@ -26,6 +26,9 @@ # Set the conda prefix directory conda_prefix = Path(utils.get_download_dir()) / "conda" +# Set templateflow directory +os.environ['TEMPLATEFLOW_HOME'] = str(Path(utils.get_download_dir()) / "templateflow") + # Set the environment variable SNAKEMAKE_CONDA_PREFIX if not already set if "SNAKEMAKE_CONDA_PREFIX" not in os.environ: os.environ["SNAKEMAKE_CONDA_PREFIX"] = str(conda_prefix) diff --git a/autoafids/workflow/rules/cnn.smk b/autoafids/workflow/rules/cnn.smk index cc096c3..ba1ec40 100644 --- a/autoafids/workflow/rules/cnn.smk +++ b/autoafids/workflow/rules/cnn.smk @@ -12,8 +12,8 @@ rule download_cnn_model: suffix="downlaod_model.log", ), shell: - "wget -q https://{params.url} -O model.zip && " - " unzip -q -d {output.unzip_dir} model.zip && " + "wget https://{params.url} -O model.zip && " + " unzip -q -d {output.unzip_dir} model.zip || true && " " rm model.zip" diff --git a/autoafids/workflow/rules/regqc.smk b/autoafids/workflow/rules/regqc.smk index 84c67fe..c59c740 100644 --- a/autoafids/workflow/rules/regqc.smk +++ b/autoafids/workflow/rules/regqc.smk @@ -109,8 +109,11 @@ def get_resampled_im(subject): def get_ref_paths(): if template_name: - refimage=directory(Path(download_dir) / "templateflow" / template_name) - refcoordinate=template_dict[template_name] + refimage=directory(Path(download_dir) / "templateflow") + + refcoordinate=str( + Path(workflow.basedir).parent / template_dict[template_name] + ) else: if lead_dbs_dir: refimage = str( @@ -128,16 +131,11 @@ rule download_template: params: template=template_name, output: - template_dir=directory(Path(download_dir) / "templateflow"), - log: - bids( - root="logs", - suffix="downlaod_template.log", - ), + template_path=directory(Path(download_dir) / "templateflow") conda: "../envs/templateflow.yaml" script: - "../scripts/templateflow.py" + "../scripts/template_flow.py" rule regqc: input: @@ -153,6 +151,8 @@ rule regqc: optional_matrix=lambda wildcards: get_optional_matrix_path( wildcards.subject ), + refim_dir=lambda wildcards: get_ref_paths()[0], + refcoord=lambda wildcards: get_ref_paths()[1], output: html=bids( root=root, @@ -176,8 +176,7 @@ rule regqc: **inputs[config["modality"]].wildcards ), params: - refim=lambda wildcards: get_ref_paths()[0], - refcoord=lambda wildcards: get_ref_paths()[1], + template=template_name, conda: "../envs/regqc.yaml" script: diff --git a/autoafids/workflow/scripts/regqc.py b/autoafids/workflow/scripts/regqc.py index 28d7f80..c0c15d8 100644 --- a/autoafids/workflow/scripts/regqc.py +++ b/autoafids/workflow/scripts/regqc.py @@ -684,12 +684,13 @@ def render_dashboard_html( # --- MAIN WRAPPER --- def generate_afid_qc_dashboard( + template_name, gt_fcsv_path, pred_fcsv_path, output_html_path, output_fcsv_path, output_csv_path,subject_nii, - template_nii, + template_dir, matfile_path, warpfile_path ): @@ -711,6 +712,8 @@ def generate_afid_qc_dashboard( "dz (mm)": dz, "ED (mm)": ed }) + + template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_res-01_T1w.nii.gz') error_df.to_csv(output_csv_path, index=False) heatmap_html = make_toggleable_heatmap([dx, dy, dz, ed], afid_ids) scatter_html = make_3d_plot(gt_coords, pred_coords, afid_ids) @@ -722,13 +725,14 @@ def generate_afid_qc_dashboard( if __name__ == "__main__": generate_afid_qc_dashboard( + template_name=snakemake.params['template'], gt_fcsv_path=snakemake.input["afidfcsv"], - pred_fcsv_path=snakemake.params["refcoord"], + pred_fcsv_path=snakemake.input["refcoord"], output_html_path=snakemake.output["html"], output_fcsv_path=snakemake.output["fcsv"], output_csv_path=snakemake.output["csv"], subject_nii=snakemake.input["im"], - template_nii=snakemake.params["refim"], + template_dir=snakemake.input["refim_dir"], matfile_path=snakemake.input["optional_matrix"], warpfile_path=snakemake.input["warp"] ) diff --git a/autoafids/workflow/scripts/template_flow.py b/autoafids/workflow/scripts/template_flow.py new file mode 100644 index 0000000..6c01597 --- /dev/null +++ b/autoafids/workflow/scripts/template_flow.py @@ -0,0 +1,5 @@ +from templateflow import api as tflow + +template_name = snakemake.params["template"] + +template_path = tflow.get(str(template_name), desc=None, resolution=1, suffix='T1w', extension='nii.gz') diff --git a/autoafids/workflow/scripts/templateflow.py b/autoafids/workflow/scripts/templateflow.py deleted file mode 100644 index 6bcb0aa..0000000 --- a/autoafids/workflow/scripts/templateflow.py +++ /dev/null @@ -1,9 +0,0 @@ -import os -from templateflow import api as tflow - -template_name = snakemake.params["template"] -output_dir = snakemake.output["template_dir"] - -os.environ['TEMPLATEFLOW_HOME'] = output_dir - -tflow.get(template_name, desc=None, resolution=1, suffix='T1w', extension='nii.gz') \ No newline at end of file From 1b2feda9eb11ae3bd48cb94f919ecc82cfaa6768 Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Tue, 13 Jan 2026 13:55:11 -0500 Subject: [PATCH 4/9] add conditional logic to work with different templates --- autoafids/config/snakebids.yml | 2 +- autoafids/workflow/scripts/regqc.py | 7 ++++++- autoafids/workflow/scripts/template_flow.py | 5 ++++- 3 files changed, 11 insertions(+), 3 deletions(-) diff --git a/autoafids/config/snakebids.yml b/autoafids/config/snakebids.yml index b28eb59..2afd30c 100644 --- a/autoafids/config/snakebids.yml +++ b/autoafids/config/snakebids.yml @@ -149,7 +149,7 @@ parse_args: --template-flow: help: 'Downloads a template from templateflow and uses it to assess the quality of registration.' - choices: ['Agile12v2016', 'MNI152Lin ', 'MNI152NLin2009cAsym', 'MNI152NLin6Sym', 'OASIS30ANTs', 'BigBrainSym' , 'MNI152NLin2009bAsym', 'MNI152NLin2009cSym', 'MNI305', 'PD25', 'fsaverage', 'MNI152NLin2009bSym', 'MNI152NLin6Asym','MNIColin27'] + choices: ['Agile12v2016', 'MNI152Lin', 'MNI152NLin2009cAsym', 'MNI152NLin6Sym', 'OASIS30ANTs', 'BigBrainSym' , 'MNI152NLin2009bAsym', 'MNI152NLin2009cSym', 'MNI305', 'PD25', 'fsaverage', 'MNI152NLin2009bSym', 'MNI152NLin6Asym','MNIColin27'] default: false required: false type: str diff --git a/autoafids/workflow/scripts/regqc.py b/autoafids/workflow/scripts/regqc.py index c0c15d8..499d719 100644 --- a/autoafids/workflow/scripts/regqc.py +++ b/autoafids/workflow/scripts/regqc.py @@ -713,7 +713,12 @@ def generate_afid_qc_dashboard( "ED (mm)": ed }) - template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_res-01_T1w.nii.gz') + if template_name in ['MNI152NLin2009bAsym','MNI152NLin2009bSym']: + template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_res-1_T1w.nii.gz') + elif template_name in ['MNI305', 'MNIColin27']: + template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_T1w.nii.gz') + else: + template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_res-01_T1w.nii.gz') error_df.to_csv(output_csv_path, index=False) heatmap_html = make_toggleable_heatmap([dx, dy, dz, ed], afid_ids) scatter_html = make_3d_plot(gt_coords, pred_coords, afid_ids) diff --git a/autoafids/workflow/scripts/template_flow.py b/autoafids/workflow/scripts/template_flow.py index 6c01597..dce4815 100644 --- a/autoafids/workflow/scripts/template_flow.py +++ b/autoafids/workflow/scripts/template_flow.py @@ -2,4 +2,7 @@ template_name = snakemake.params["template"] -template_path = tflow.get(str(template_name), desc=None, resolution=1, suffix='T1w', extension='nii.gz') +if template_name in ['MNI305', 'MNIColin27']: + template_path = tflow.get(str(template_name), desc=None, suffix='T1w', extension='nii.gz') +else: + template_path = tflow.get(str(template_name), desc=None, resolution=1, suffix='T1w', extension='nii.gz') From 355f56cb20c57379bc87ed8f233d5ee16d8b7d72 Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Fri, 16 Jan 2026 08:38:35 -0500 Subject: [PATCH 5/9] fix ruff linting error --- autoafids/run.py | 4 ++- autoafids/workflow/scripts/regqc.py | 28 +++++++++++++++------ autoafids/workflow/scripts/template_flow.py | 15 +++++++++-- 3 files changed, 37 insertions(+), 10 deletions(-) diff --git a/autoafids/run.py b/autoafids/run.py index 94a058c..47063de 100755 --- a/autoafids/run.py +++ b/autoafids/run.py @@ -27,7 +27,9 @@ conda_prefix = Path(utils.get_download_dir()) / "conda" # Set templateflow directory -os.environ['TEMPLATEFLOW_HOME'] = str(Path(utils.get_download_dir()) / "templateflow") +os.environ['TEMPLATEFLOW_HOME'] = str( + Path(utils.get_download_dir()) / "templateflow" + ) # Set the environment variable SNAKEMAKE_CONDA_PREFIX if not already set if "SNAKEMAKE_CONDA_PREFIX" not in os.environ: diff --git a/autoafids/workflow/scripts/regqc.py b/autoafids/workflow/scripts/regqc.py index 499d719..6414431 100644 --- a/autoafids/workflow/scripts/regqc.py +++ b/autoafids/workflow/scripts/regqc.py @@ -109,7 +109,11 @@ def apply_affine_transform(mat_path, coords): return transformed_homogeneous[:, :3] # --- APPLY WARP (HARMONIZED) --- -def apply_warp_deformation(transform_path, coords, flip_ras_lps=True, leaddbs=True): +def apply_warp_deformation( + transform_path, + coords, + flip_ras_lps=True, + leaddbs=True): """ Applies a non-linear warp deformation to coordinates using a SimpleITK displacement field. @@ -136,10 +140,12 @@ def apply_warp_deformation(transform_path, coords, flip_ras_lps=True, leaddbs=Tr transformed_coords = np.array([ transform.TransformPoint(point.tolist()) for point in coords ]) - + else: d = pd.DataFrame(data=coords, columns=['x','y','z']) - transformed_coords_dataframe = ants.apply_transforms_to_points( 3, d, transform_path) + transformed_coords_dataframe = ants.apply_transforms_to_points( 3, + d, + transform_path) transformed_coords = transformed_coords_dataframe.to_numpy() if flip_ras_lps: @@ -699,7 +705,9 @@ def generate_afid_qc_dashboard( gt_coords_a= apply_affine_transform(matfile_path,native_coords) gt_coords= apply_warp_deformation(warpfile_path,gt_coords_a) else: - gt_coords= apply_warp_deformation(warpfile_path,native_coords, leaddbs=False) + gt_coords= apply_warp_deformation(warpfile_path, + native_coords, + leaddbs=False) pred_coords, _ = load_fcsv(pred_fcsv_path) afids_to_fcsv(gt_coords, output_fcsv_path) dx, dy, dz, ed = compute_error_components(gt_coords, pred_coords) @@ -714,11 +722,17 @@ def generate_afid_qc_dashboard( }) if template_name in ['MNI152NLin2009bAsym','MNI152NLin2009bSym']: - template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_res-1_T1w.nii.gz') + template_nii = str(Path(template_dir) / + f'tpl-{template_name}' / + f'tpl-{template_name}_res-1_T1w.nii.gz') elif template_name in ['MNI305', 'MNIColin27']: - template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_T1w.nii.gz') + template_nii = str(Path(template_dir) / + f'tpl-{template_name}' / + f'tpl-{template_name}_T1w.nii.gz') else: - template_nii = str(Path(template_dir) / f'tpl-{template_name}' / f'tpl-{template_name}_res-01_T1w.nii.gz') + template_nii = str(Path(template_dir) / + f'tpl-{template_name}' / + f'tpl-{template_name}_res-01_T1w.nii.gz') error_df.to_csv(output_csv_path, index=False) heatmap_html = make_toggleable_heatmap([dx, dy, dz, ed], afid_ids) scatter_html = make_3d_plot(gt_coords, pred_coords, afid_ids) diff --git a/autoafids/workflow/scripts/template_flow.py b/autoafids/workflow/scripts/template_flow.py index dce4815..c1dd350 100644 --- a/autoafids/workflow/scripts/template_flow.py +++ b/autoafids/workflow/scripts/template_flow.py @@ -3,6 +3,17 @@ template_name = snakemake.params["template"] if template_name in ['MNI305', 'MNIColin27']: - template_path = tflow.get(str(template_name), desc=None, suffix='T1w', extension='nii.gz') + template_path = tflow.get( + str(template_name), + desc=None, + suffix='T1w', + extension='nii.gz' + ) else: - template_path = tflow.get(str(template_name), desc=None, resolution=1, suffix='T1w', extension='nii.gz') + template_path = tflow.get( + str(template_name), + desc=None, + resolution=1, + suffix='T1w', + extension='nii.gz' + ) From 651564df46cd500587f6766879c4d4488b1b70b5 Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Fri, 16 Jan 2026 08:41:10 -0500 Subject: [PATCH 6/9] fix snakefmt linting --- autoafids/workflow/rules/regqc.smk | 46 +++++++++++++++++------------- 1 file changed, 26 insertions(+), 20 deletions(-) diff --git a/autoafids/workflow/rules/regqc.smk b/autoafids/workflow/rules/regqc.smk index c59c740..98e355b 100644 --- a/autoafids/workflow/rules/regqc.smk +++ b/autoafids/workflow/rules/regqc.smk @@ -4,23 +4,23 @@ import glob lead_dbs_dir = config.get("LEAD_DBS_DIR", False) fmriprep_dir = config.get("FMRIPREP_DIR", False) -template_name = config.get("template_flow", '') +template_name = config.get("template_flow", "") template_dict = { - "Agile12v2016" : 'resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv', - "MNI152Lin" : 'resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv', - "MNI152NLin2009cAsym" : 'resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv', - "MNI152NLin6Sym" : 'resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv', - "OASIS30ANTs" : 'resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv', - "BigBrainSym" : 'resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv', - "MNI152NLin2009bAsym" : 'resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv', - "MNI152NLin2009cSym" : 'resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv', - "MNI305" : 'resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv', - "PD25" : 'resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv', - "fsaverage" : 'resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv', - "MNI152NLin2009bSym" : 'resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv', - "MNI152NLin6Asym" : 'resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv', - "MNIColin27" : 'resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv', + "Agile12v2016": "resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv", + "MNI152Lin": "resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv", + "MNI152NLin2009cAsym": "resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv", + "MNI152NLin6Sym": "resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv", + "OASIS30ANTs": "resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv", + "BigBrainSym": "resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv", + "MNI152NLin2009bAsym": "resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv", + "MNI152NLin2009cSym": "resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv", + "MNI305": "resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv", + "PD25": "resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv", + "fsaverage": "resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv", + "MNI152NLin2009bSym": "resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv", + "MNI152NLin6Asym": "resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv", + "MNIColin27": "resources/regqc/tpl-MNIColin27_desc-groundtruth_afids.fcsv", } @@ -109,9 +109,9 @@ def get_resampled_im(subject): def get_ref_paths(): if template_name: - refimage=directory(Path(download_dir) / "templateflow") + refimage = directory(Path(download_dir) / "templateflow") - refcoordinate=str( + refcoordinate = str( Path(workflow.basedir).parent / template_dict[template_name] ) else: @@ -123,20 +123,26 @@ def get_ref_paths(): Path(workflow.basedir).parent / config["fcsv_mni_lead"] ) else: - refimage = str(Path(workflow.basedir).parent / config["templatet1w"]) - refcoordinate = str(Path(workflow.basedir).parent / config["fcsv_mni"]) + refimage = str( + Path(workflow.basedir).parent / config["templatet1w"] + ) + refcoordinate = str( + Path(workflow.basedir).parent / config["fcsv_mni"] + ) return refimage, refcoordinate + rule download_template: params: template=template_name, output: - template_path=directory(Path(download_dir) / "templateflow") + template_path=directory(Path(download_dir) / "templateflow"), conda: "../envs/templateflow.yaml" script: "../scripts/template_flow.py" + rule regqc: input: afidfcsv=bids( From 3b5684e7a3ed6b46f6cf68bd8cc948ac55eccaff Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Fri, 16 Jan 2026 11:10:02 -0500 Subject: [PATCH 7/9] delete unsupported templates and patch the logic to template path --- autoafids/config/snakebids.yml | 2 +- ...ce-ICBM2009sym_desc-groundtruth_afids.fcsv | 35 ------------------- ...l-Agile12v2016_desc-groundtruth_afids.fcsv | 35 ------------------- ...009bAsym_res-1_desc-groundtruth_afids.fcsv | 35 ------------------- ...pl-PD25-res-01_desc-groundtruth_afids.fcsv | 35 ------------------- autoafids/workflow/rules/regqc.smk | 6 +--- autoafids/workflow/scripts/regqc.py | 31 +++++++++------- 7 files changed, 20 insertions(+), 159 deletions(-) delete mode 100644 autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv delete mode 100644 autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv delete mode 100644 autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv delete mode 100644 autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv diff --git a/autoafids/config/snakebids.yml b/autoafids/config/snakebids.yml index 2afd30c..0c9b5b8 100644 --- a/autoafids/config/snakebids.yml +++ b/autoafids/config/snakebids.yml @@ -149,7 +149,7 @@ parse_args: --template-flow: help: 'Downloads a template from templateflow and uses it to assess the quality of registration.' - choices: ['Agile12v2016', 'MNI152Lin', 'MNI152NLin2009cAsym', 'MNI152NLin6Sym', 'OASIS30ANTs', 'BigBrainSym' , 'MNI152NLin2009bAsym', 'MNI152NLin2009cSym', 'MNI305', 'PD25', 'fsaverage', 'MNI152NLin2009bSym', 'MNI152NLin6Asym','MNIColin27'] + choices: ['MNI152Lin', 'MNI152NLin2009cAsym', 'MNI152NLin6Sym', 'OASIS30ANTs', 'MNI152NLin2009cSym', 'MNI305', 'fsaverage', 'MNI152NLin2009bSym', 'MNI152NLin6Asym','MNIColin27'] default: false required: false type: str diff --git a/autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv deleted file mode 100644 index 888e7e7..0000000 --- a/autoafids/resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv +++ /dev/null @@ -1,35 +0,0 @@ -# Markups fiducial file version = 4.6 -# CoordinateSystem = 0 -# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID -vtkMRMLMarkupsFiducialNode_1,0.265,2.6205,-4.1925,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_2,0.1965,-25.3475,-2.4835,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_3,0.4325,-39.0585,-16.3025,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_4,0.465,-22.9715,-21.68,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_5,0.1885,-12.8125,-10.9745,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_6,12.7105,-27.041,-10.1395,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_7,-12.4665,-27.064,-10.7585,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_8,10.599,-30.311,-22.488,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_9,-10.1095,-30.4125,-23.7145,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_10,0.181,-43.383,4.344,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_11,-0.1555,-7.959,-14.9365,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_12,2.513,-7.9635,-13.463,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_13,-2.853,-8.271,-13.936,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_14,0.2725,-34.4745,3.558,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_15,16.213,4.4325,25.801,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_16,-16.143,4.4655,25.685,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_17,19.58,-23.463,28.507,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_18,-19.666,-23.452,27.885,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_19,0.025,33.2105,3.1305,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_20,0.563,-39.4115,7.6585,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_21,34.341,-4.7005,-26.1515,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_22,-33.368,-5.6025,-22.4175,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_23,17.6445,-10.098,-18.0085,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_24,-18.851,-9.6085,-19.1485,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_25,20.57,-5.055,-27.248,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_26,-19.613,-5.212,-26.086,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_27,12.5145,-43.3165,6.002,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_28,-13.21,-43.0065,6.5705,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_29,19.5905,-83.6925,3.927,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_30,-18.1015,-84.7275,-0.1355,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_31,12.4725,20.1715,-11.854,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_32,-12.385,20.7985,-11.4635,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv deleted file mode 100644 index a092607..0000000 --- a/autoafids/resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv +++ /dev/null @@ -1,35 +0,0 @@ -# Markups fiducial file version = 4.6 -# CoordinateSystem = 0 -# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID -vtkMRMLMarkupsFiducialNode_1,4.1493909375,5.678821875,1.4795320625,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_2,3.230568125,-19.9064125,-4.8756628125,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_3,2.7960728125,-28.60988125,-16.037834375,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_4,3.421190625,-13.23296875,-20.471746875,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_5,3.7356490625,-7.0098490625,-8.73979625,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_6,15.00718125,-18.92895,-11.42105,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_7,-8.9887453125,-18.22670625,-11.611440625,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_8,12.9510625,-19.957878125,-22.0481875,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_9,-6.58012,-18.918334375,-21.962928125,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_10,1.9017196875,-45.484784375,-8.999916875,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_11,4.1233628125,-0.9788696875,-10.8898759375,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_12,6.2728634375,-1.11923546875,-10.12487625,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_13,2.0539009375,-1.0529093125,-10.1125115625,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_14,2.7084884375,-25.85953125,-4.796835625,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_15,18.588353125,-1.43555084375,27.09186875,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_16,-10.36823125,-0.48472604996875,26.8761625,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_17,19.9445125,-27.044696875,20.790275,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_18,-14.211640625,-25.8343,20.192028125,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_19,5.6998965625,30.37541875,17.899746875,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_20,2.7595959375,-33.2157875,-1.4735090625,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_21,34.593409375,4.67608296875,-19.13281875,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_22,-26.09055,5.6104065625,-18.54696875,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_23,20.01790625,-2.7720371875,-12.648403125,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_24,-12.713090625,-1.5686535,-13.346115625,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_25,23.83704375,5.44529328125,-20.423478125,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_26,-15.429971875,6.27710625,-20.405490625,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_27,15.39044375,-36.3536625,-4.7835621875,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_28,-11.80639375,-36.848665625,-5.417424375,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_29,17.988434375,-72.19396875,-15.9282,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_30,-17.312128125,-72.209359375,-16.6732875,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_31,16.650659375,21.919425,1.23355321875,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_32,-6.7836909375,22.16438125,-0.05127345,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv deleted file mode 100644 index 4ef3056..0000000 --- a/autoafids/resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv +++ /dev/null @@ -1,35 +0,0 @@ -# Markups fiducial file version = 4.6 -# CoordinateSystem = 0 -# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID -vtkMRMLMarkupsFiducialNode_1,-0.204861407692308,2.72288076923077,-4.88105282051282,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_2,-0.00726026948717949,-25.0450538461538,-2.21068230769231,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_3,0.025998141025641,-37.691917948718,-11.0111497435897,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_4,-0.0892198512820513,-23.1885743589744,-21.5288358974359,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_5,-0.05649251,-13.7676564102564,-10.950028974359,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_6,13.3113025641026,-25.951058974359,-9.74885435897436,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_7,-13.607458974359,-26.4451,-9.7076082051282,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_8,10.8321820512821,-30.8104076923077,-21.5949358974359,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_9,-10.9824102564103,-30.8778025641026,-21.4372025641026,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_10,0.0100564897435897,-52.5094615384615,2.14842435897436,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_11,-0.0743417574102564,-8.36030051282051,-15.9354820512821,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_12,2.02761256410256,-8.15453153846154,-15.0245538461538,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_13,-2.19342487179487,-8.21593282051282,-15.0426743589744,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_14,0.00940744421052632,-31.5985789473684,0.568596455263158,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_15,15.1850526315789,5.61940868421053,24.9488552631579,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_16,-15.7984342105263,5.47038342105263,25.0905473684211,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_17,18.7231289473684,-22.0626210526316,28.0333394736842,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_18,-18.4848157894737,-22.2426736842105,28.1745157894737,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_19,-0.111086676315789,33.3615236842105,2.12355523157895,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_20,0.116840065,-37.6019447368421,6.49650894736842,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_21,34.0034921052632,-4.056905,-27.3505,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_22,-34.8327763157895,-6.646575,-25.3468578947368,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_23,17.4263131578947,-10.0524047368421,-18.2650921052632,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_24,-18.1468184210526,-10.9803721052632,-18.3750131578947,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_25,20.4641447368421,-4.03479921052632,-28.0214973684211,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_26,-21.3443842105263,-5.12460973684211,-27.9912052631579,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_27,14.6365184210526,-40.7174131578947,4.71004973684211,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_28,-14.8907842105263,-43.0901605263158,4.23491921052632,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_29,20.8308868421053,-79.2528368421053,4.51120236842105,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_30,-18.9085052631579,-82.82955,3.54751710526316,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_31,11.8931421052632,18.5102315789474,-12.3773210526316,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_32,-13.3650815789474,17.0294973684211,-13.0638105263158,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv b/autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv deleted file mode 100644 index bf21410..0000000 --- a/autoafids/resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv +++ /dev/null @@ -1,35 +0,0 @@ -# Markups fiducial file version = 4.10 -# CoordinateSystem = 0 -# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID -vtkMRMLMarkupsFiducialNode_1,-0.23650000000000002,3.362,-3.64,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_2,-0.181,-25.177,-1.0295,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_3,-0.051,-36.6575,-9.397,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_4,-0.147,-23.484499999999997,-19.863500000000002,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_5,0.0,-14.456,-9.4235,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_6,13.243500000000001,-25.8875,-8.621500000000001,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_7,-13.995000000000001,-26.308999999999997,-8.4855,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_8,10.722,-31.064,-19.9825,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_9,-11.2515,-30.956000000000003,-19.9625,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_10,-0.362,-52.185500000000005,2.6505,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_11,-0.1765,-7.6645,-13.91,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_12,2.0845000000000002,-8.0915,-12.946,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_13,-2.621,-7.977499999999999,-12.905000000000001,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_14,-0.4595,-32.0995,1.825,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_15,16.070999999999998,7.5855,25.072499999999998,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_16,-16.5295,7.5005,25.117,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_17,18.744,-24.8485,29.307499999999997,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_18,-18.878,-25.000500000000002,28.9835,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_19,-0.021500000000000005,34.516999999999996,1.5135,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_20,-0.118,-37.42,8.0315,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_21,34.439499999999995,-4.3065,-26.737000000000002,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_22,-35.7425,-7.0745000000000005,-25.0885,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_23,18.9895,-10.061499999999999,-16.5675,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_24,-20.787,-11.126,-16.436,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_25,21.685,-4.7955000000000005,-29.0085,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_26,-23.0095,-5.751,-28.208,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_27,16.473,-41.2255,4.532500000000001,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_28,-15.3925,-43.3945,4.894500000000001,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_29,20.567999999999998,-77.83099999999999,5.7245,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_30,-19.775,-80.1425,6.2545,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_31,11.855,19.5445,-13.033000000000001,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 -vtkMRMLMarkupsFiducialNode_32,-13.587499999999999,17.979,-13.321,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1 diff --git a/autoafids/workflow/rules/regqc.smk b/autoafids/workflow/rules/regqc.smk index 98e355b..fe6074e 100644 --- a/autoafids/workflow/rules/regqc.smk +++ b/autoafids/workflow/rules/regqc.smk @@ -7,16 +7,12 @@ fmriprep_dir = config.get("FMRIPREP_DIR", False) template_name = config.get("template_flow", "") template_dict = { - "Agile12v2016": "resources/regqc/tpl-Agile12v2016_desc-groundtruth_afids.fcsv", "MNI152Lin": "resources/regqc/tpl-MNI152Lin_res-01_desc-groundtruth_afids.fcsv", "MNI152NLin2009cAsym": "resources/regqc/tpl-MNI152NLin2009cAsym_res-01_desc-groundtruth_afids.fcsv", "MNI152NLin6Sym": "resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv", "OASIS30ANTs": "resources/regqc/tpl-OASIS30ANTs_res-01_desc-groundtruth_afids.fcsv", - "BigBrainSym": "resources/regqc/BigBrain_space-ICBM2009sym_desc-groundtruth_afids.fcsv", - "MNI152NLin2009bAsym": "resources/regqc/tpl-MNI152NLin2009bAsym_res-1_desc-groundtruth_afids.fcsv", "MNI152NLin2009cSym": "resources/regqc/tpl-MNI152NLin2009cSym_res-1_desc-groundtruth_afids.fcsv", "MNI305": "resources/regqc/tpl-MNI305_desc-groundtruth_afids.fcsv", - "PD25": "resources/regqc/tpl-PD25-res-01_desc-groundtruth_afids.fcsv", "fsaverage": "resources/regqc/tpl-fsaverage_res-01_den-41k_desc-groundtruth_afids.fcsv", "MNI152NLin2009bSym": "resources/regqc/tpl-MNI152NLin2009bSym_res-1_desc-groundtruth_afids.fcsv", "MNI152NLin6Asym": "resources/regqc/tpl-MNI152NLin6Asym_res-01_desc-groundtruth_afids.fcsv", @@ -157,7 +153,7 @@ rule regqc: optional_matrix=lambda wildcards: get_optional_matrix_path( wildcards.subject ), - refim_dir=lambda wildcards: get_ref_paths()[0], + refim=lambda wildcards: get_ref_paths()[0], refcoord=lambda wildcards: get_ref_paths()[1], output: html=bids( diff --git a/autoafids/workflow/scripts/regqc.py b/autoafids/workflow/scripts/regqc.py index 6414431..9442626 100644 --- a/autoafids/workflow/scripts/regqc.py +++ b/autoafids/workflow/scripts/regqc.py @@ -696,7 +696,7 @@ def generate_afid_qc_dashboard( output_html_path, output_fcsv_path, output_csv_path,subject_nii, - template_dir, + template_path_or_dir, matfile_path, warpfile_path ): @@ -721,18 +721,23 @@ def generate_afid_qc_dashboard( "ED (mm)": ed }) - if template_name in ['MNI152NLin2009bAsym','MNI152NLin2009bSym']: - template_nii = str(Path(template_dir) / - f'tpl-{template_name}' / - f'tpl-{template_name}_res-1_T1w.nii.gz') - elif template_name in ['MNI305', 'MNIColin27']: - template_nii = str(Path(template_dir) / - f'tpl-{template_name}' / - f'tpl-{template_name}_T1w.nii.gz') + if template_name: + if template_name in ['MNI152NLin2009bAsym','MNI152NLin2009bSym']: + template_nii = str(Path(template_path_or_dir) / + f'tpl-{template_name}' / + f'tpl-{template_name}_res-1_T1w.nii.gz') + elif template_name in ['MNI305', 'MNIColin27']: + template_nii = str(Path(template_path_or_dir) / + f'tpl-{template_name}' / + f'tpl-{template_name}_T1w.nii.gz') + else: + template_nii = str(Path(template_path_or_dir) / + f'tpl-{template_name}' / + f'tpl-{template_name}_res-01_T1w.nii.gz') else: - template_nii = str(Path(template_dir) / - f'tpl-{template_name}' / - f'tpl-{template_name}_res-01_T1w.nii.gz') + template_nii = template_path_or_dir + + error_df.to_csv(output_csv_path, index=False) heatmap_html = make_toggleable_heatmap([dx, dy, dz, ed], afid_ids) scatter_html = make_3d_plot(gt_coords, pred_coords, afid_ids) @@ -751,7 +756,7 @@ def generate_afid_qc_dashboard( output_fcsv_path=snakemake.output["fcsv"], output_csv_path=snakemake.output["csv"], subject_nii=snakemake.input["im"], - template_dir=snakemake.input["refim_dir"], + template_path_or_dir=snakemake.input["refim"], matfile_path=snakemake.input["optional_matrix"], warpfile_path=snakemake.input["warp"] ) From 0273fd41d16d4716cc0d594e2b6db94067514de6 Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Mon, 19 Jan 2026 08:48:52 -0500 Subject: [PATCH 8/9] fix ruff lint check --- autoafids/workflow/scripts/regqc.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/autoafids/workflow/scripts/regqc.py b/autoafids/workflow/scripts/regqc.py index 9442626..3b7835b 100644 --- a/autoafids/workflow/scripts/regqc.py +++ b/autoafids/workflow/scripts/regqc.py @@ -736,8 +736,8 @@ def generate_afid_qc_dashboard( f'tpl-{template_name}_res-01_T1w.nii.gz') else: template_nii = template_path_or_dir - - + + error_df.to_csv(output_csv_path, index=False) heatmap_html = make_toggleable_heatmap([dx, dy, dz, ed], afid_ids) scatter_html = make_3d_plot(gt_coords, pred_coords, afid_ids) From 3d55482c4f62ccc7497c46c4b7499cd6502f676d Mon Sep 17 00:00:00 2001 From: Dhananjhay Date: Mon, 19 Jan 2026 09:23:32 -0500 Subject: [PATCH 9/9] remove snakemake_timestamps from osf storage and the conditional true statements from unzip --- autoafids/workflow/rules/cnn.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/autoafids/workflow/rules/cnn.smk b/autoafids/workflow/rules/cnn.smk index ba1ec40..1abb9e0 100644 --- a/autoafids/workflow/rules/cnn.smk +++ b/autoafids/workflow/rules/cnn.smk @@ -13,7 +13,7 @@ rule download_cnn_model: ), shell: "wget https://{params.url} -O model.zip && " - " unzip -q -d {output.unzip_dir} model.zip || true && " + " unzip -q -d {output.unzip_dir} model.zip && " " rm model.zip"