nipype · tclose · Nov 2, 2023 · Nov 2, 2023 · Nov 2, 2023 · Nov 2, 2023
diff --git a/workflows/pythonpackage.yaml → .github/workflows/pythonpackage.yaml b/workflows/pythonpackage.yaml → .github/workflows/pythonpackage.yaml
@@ -93,6 +93,10 @@ jobs:
       with:
         name: converted-nipype
         path: pydra/tasks/freesurfer/auto
+    - name: Check directory structure
+      run: |
+        sudo apt install tree
+        tree .
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:

diff --git a/nipype-auto-conv/specs/add_x_form_to_header.yaml b/nipype-auto-conv/specs/add_x_form_to_header.yaml
@@ -32,7 +32,7 @@
 #     [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header]
 # 
 #     
-task_name: add_x_form_to_header
+task_name: AddXFormToHeader
 nipype_name: AddXFormToHeader
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/aparc_2_aseg.yaml b/nipype-auto-conv/specs/aparc_2_aseg.yaml
@@ -41,7 +41,7 @@
 #     'mri_aparc2aseg --labelwm  --o aparc+aseg.mgz --rip-unknown --s subject_id'
 # 
 #     
-task_name: aparc_2_aseg
+task_name: Aparc2Aseg
 nipype_name: Aparc2Aseg
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/apas_2_aseg.yaml b/nipype-auto-conv/specs/apas_2_aseg.yaml
@@ -21,7 +21,7 @@
 #     'apas2aseg --i aseg.mgz --o output.mgz'
 # 
 #     
-task_name: apas_2_aseg
+task_name: Apas2Aseg
 nipype_name: Apas2Aseg
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/apply_mask.yaml b/nipype-auto-conv/specs/apply_mask.yaml
@@ -12,7 +12,7 @@
 #     space with an LTA matrix.
 # 
 #     
-task_name: apply_mask
+task_name: ApplyMask
 nipype_name: ApplyMask
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/apply_vol_transform.yaml b/nipype-auto-conv/specs/apply_vol_transform.yaml
@@ -20,7 +20,7 @@
 #     'mri_vol2vol --fstarg --reg register.dat --mov structural.nii --o struct_warped.nii'
 # 
 #     
-task_name: apply_vol_transform
+task_name: ApplyVolTransform
 nipype_name: ApplyVolTransform
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/bb_register.yaml b/nipype-auto-conv/specs/bb_register.yaml
@@ -20,7 +20,7 @@
 #     'bbregister --t2 --init-header --reg structural_bbreg_me.dat --mov structural.nii --s me'
 # 
 #     
-task_name: bb_register
+task_name: BBRegister
 nipype_name: BBRegister
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/binarize.yaml b/nipype-auto-conv/specs/binarize.yaml
@@ -14,7 +14,7 @@
 #     'mri_binarize --o foo_out.nii --i structural.nii --min 10.000000'
 # 
 #     
-task_name: binarize
+task_name: Binarize
 nipype_name: Binarize
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/ca_label.yaml b/nipype-auto-conv/specs/ca_label.yaml
@@ -24,7 +24,7 @@
 #     'mri_ca_label norm.mgz trans.mat Template_6.nii out.mgz'
 # 
 #     
-task_name: ca_label
+task_name: CALabel
 nipype_name: CALabel
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/ca_normalize.yaml b/nipype-auto-conv/specs/ca_normalize.yaml
@@ -24,7 +24,7 @@
 #     'mri_ca_normalize T1.mgz atlas.nii.gz trans.mat T1_norm.mgz'
 # 
 #     
-task_name: ca_normalize
+task_name: CANormalize
 nipype_name: CANormalize
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/ca_register.yaml b/nipype-auto-conv/specs/ca_register.yaml
@@ -22,7 +22,7 @@
 #     'mri_ca_register norm.mgz talairach.m3z'
 # 
 #     
-task_name: ca_register
+task_name: CARegister
 nipype_name: CARegister
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/check_talairach_alignment.yaml b/nipype-auto-conv/specs/check_talairach_alignment.yaml
@@ -21,7 +21,7 @@
 # 
 #     >>> checker.run() # doctest: +SKIP
 #     
-task_name: check_talairach_alignment
+task_name: CheckTalairachAlignment
 nipype_name: CheckTalairachAlignment
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/concatenate.yaml b/nipype-auto-conv/specs/concatenate.yaml
@@ -20,7 +20,7 @@
 #     'mri_concat --o bar.nii --i cont1.nii --i cont2.nii'
 # 
 #     
-task_name: concatenate
+task_name: Concatenate
 nipype_name: Concatenate
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/concatenate_lta.yaml b/nipype-auto-conv/specs/concatenate_lta.yaml
@@ -33,7 +33,7 @@
 #     >>> conc_lta.cmdline
 #     'mri_concatenate_lta -invert1 -out_type 1 lta1.lta identity.nofile inv1.lta'
 #     
-task_name: concatenate_lta
+task_name: ConcatenateLTA
 nipype_name: ConcatenateLTA
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/contrast.yaml b/nipype-auto-conv/specs/contrast.yaml
@@ -23,7 +23,7 @@
 #     >>> contrast.cmdline # doctest: +SKIP
 #     'pctsurfcon --lh-only --s 10335'
 #     
-task_name: contrast
+task_name: Contrast
 nipype_name: Contrast
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/curvature.yaml b/nipype-auto-conv/specs/curvature.yaml
@@ -19,7 +19,7 @@
 #     >>> curv.cmdline
 #     'mris_curvature -w lh.pial'
 #     
-task_name: curvature
+task_name: Curvature
 nipype_name: Curvature
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/curvature_stats.yaml b/nipype-auto-conv/specs/curvature_stats.yaml
@@ -42,7 +42,7 @@
 #     >>> curvstats.cmdline
 #     'mris_curvature_stats -m -o lh.curv.stats -F pial -G --writeCurvatureFiles subject_id lh pial pial'
 #     
-task_name: curvature_stats
+task_name: CurvatureStats
 nipype_name: CurvatureStats
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/dicom_convert.yaml b/nipype-auto-conv/specs/dicom_convert.yaml
@@ -16,7 +16,7 @@
 #     >>> cvt.inputs.file_mapping = [('nifti', '*.nii'), ('info', 'dicom*.txt'), ('dti', '*dti.bv*')]
 # 
 #     
-task_name: dicom_convert
+task_name: DICOMConvert
 nipype_name: DICOMConvert
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/edit_w_mwith_aseg.yaml b/nipype-auto-conv/specs/edit_w_mwith_aseg.yaml
@@ -20,7 +20,7 @@
 #     >>> editwm.cmdline
 #     'mri_edit_wm_with_aseg -keep-in T1.mgz norm.mgz aseg.mgz wm.asegedit.mgz'
 #     
-task_name: edit_w_mwith_aseg
+task_name: EditWMwithAseg
 nipype_name: EditWMwithAseg
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/em_register.yaml b/nipype-auto-conv/specs/em_register.yaml
@@ -19,7 +19,7 @@
 #     >>> register.cmdline
 #     'mri_em_register -uns 9 -skull norm.mgz aseg.mgz norm_transform.lta'
 #     
-task_name: em_register
+task_name: EMRegister
 nipype_name: EMRegister
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/euler_number.yaml b/nipype-auto-conv/specs/euler_number.yaml
@@ -16,7 +16,7 @@
 #     >>> ft.cmdline
 #     'mris_euler_number lh.pial'
 #     
-task_name: euler_number
+task_name: EulerNumber
 nipype_name: EulerNumber
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/extract_main_component.yaml b/nipype-auto-conv/specs/extract_main_component.yaml
@@ -16,7 +16,7 @@
 #     'mris_extract_main_component lh.pial lh.maincmp'
 # 
 #     
-task_name: extract_main_component
+task_name: ExtractMainComponent
 nipype_name: ExtractMainComponent
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/fit_ms_params.yaml b/nipype-auto-conv/specs/fit_ms_params.yaml
@@ -17,7 +17,7 @@
 #     'mri_ms_fitparms  flash_05.mgz flash_30.mgz flash_parameters'
 # 
 #     
-task_name: fit_ms_params
+task_name: FitMSParams
 nipype_name: FitMSParams
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/fix_topology.yaml b/nipype-auto-conv/specs/fix_topology.yaml
@@ -24,7 +24,7 @@
 #     >>> ft.cmdline # doctest: +SKIP
 #     'mris_fix_topology -ga -mgz -sphere qsphere.nofix 10335 lh'
 #     
-task_name: fix_topology
+task_name: FixTopology
 nipype_name: FixTopology
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/fuse_segmentations.yaml b/nipype-auto-conv/specs/fuse_segmentations.yaml
@@ -20,7 +20,7 @@
 #     >>> fuse.cmdline
 #     'mri_fuse_segmentations -n norm.mgz -a aseg.mgz -c aseg.mgz tp.long.A.template tp1 tp2'
 #     
-task_name: fuse_segmentations
+task_name: FuseSegmentations
 nipype_name: FuseSegmentations
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/glm_fit.yaml b/nipype-auto-conv/specs/glm_fit.yaml
@@ -16,7 +16,7 @@
 #     True
 # 
 #     
-task_name: glm_fit
+task_name: GLMFit
 nipype_name: GLMFit
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/gtm_seg.yaml b/nipype-auto-conv/specs/gtm_seg.yaml
@@ -14,7 +14,7 @@
 #     >>> gtmseg.cmdline
 #     'gtmseg --o gtmseg.mgz --s subject_id'
 #     
-task_name: gtm_seg
+task_name: GTMSeg
 nipype_name: GTMSeg
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/gtmpvc.yaml b/nipype-auto-conv/specs/gtmpvc.yaml
@@ -33,7 +33,7 @@
 #     >>> gtmpvc.cmdline  # doctest: +NORMALIZE_WHITESPACE
 #     'mri_gtmpvc --i sub-01_ses-baseline_pet.nii.gz --mg 0.5 ROI1 ROI2 --o pvc --regheader --seg gtmseg.mgz'
 #     
-task_name: gtmpvc
+task_name: GTMPVC
 nipype_name: GTMPVC
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/jacobian.yaml b/nipype-auto-conv/specs/jacobian.yaml
@@ -17,7 +17,7 @@
 #     >>> jacobian.cmdline
 #     'mris_jacobian lh.pial lh.pial lh.jacobian'
 #     
-task_name: jacobian
+task_name: Jacobian
 nipype_name: Jacobian
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/label_2_annot.yaml b/nipype-auto-conv/specs/label_2_annot.yaml
@@ -20,7 +20,7 @@
 #     >>> l2a.cmdline
 #     'mris_label2annot --hemi lh --l lh.aparc.label --a test --s 10335'
 #     
-task_name: label_2_annot
+task_name: Label2Annot
 nipype_name: Label2Annot
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/label_2_label.yaml b/nipype-auto-conv/specs/label_2_label.yaml
@@ -31,7 +31,7 @@
 #     >>> l2l.cmdline
 #     'mri_label2label --hemi lh --trglabel lh-pial_converted.stl --regmethod surface --srclabel lh-pial.stl --srcsubject fsaverage --trgsubject 10335'
 #     
-task_name: label_2_label
+task_name: Label2Label
 nipype_name: Label2Label
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/label_2_vol.yaml b/nipype-auto-conv/specs/label_2_vol.yaml
@@ -14,7 +14,7 @@
 #     'mri_label2vol --fillthresh 0.5 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii'
 # 
 #     
-task_name: label_2_vol
+task_name: Label2Vol
 nipype_name: Label2Vol
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/make_average_subject.yaml b/nipype-auto-conv/specs/make_average_subject.yaml
@@ -16,7 +16,7 @@
 #     'make_average_subject --out average --subjects s1 s2'
 # 
 #     
-task_name: make_average_subject
+task_name: MakeAverageSubject
 nipype_name: MakeAverageSubject
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/make_surfaces.yaml b/nipype-auto-conv/specs/make_surfaces.yaml
@@ -27,7 +27,7 @@
 #     >>> makesurfaces.cmdline
 #     'mris_make_surfaces -T1 T1.mgz -orig pial -orig_pial pial 10335 lh'
 #     
-task_name: make_surfaces
+task_name: MakeSurfaces
 nipype_name: MakeSurfaces
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mni_bias_correction.yaml b/nipype-auto-conv/specs/mni_bias_correction.yaml
@@ -32,7 +32,7 @@
 #     [https://github.com/BIC-MNI/N3]
 # 
 #     
-task_name: mni_bias_correction
+task_name: MNIBiasCorrection
 nipype_name: MNIBiasCorrection
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mp_rto_mni305.yaml b/nipype-auto-conv/specs/mp_rto_mni305.yaml
@@ -26,7 +26,7 @@
 #     >>> mprtomni305.run() # doctest: +SKIP
 # 
 #     
-task_name: mp_rto_mni305
+task_name: MPRtoMNI305
 nipype_name: MPRtoMNI305
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mr_is_ca_label.yaml b/nipype-auto-conv/specs/mr_is_ca_label.yaml
@@ -30,7 +30,7 @@
 #     >>> ca_label.cmdline
 #     'mris_ca_label test lh lh.pial im1.nii lh.aparc.annot'
 #     
-task_name: mr_is_ca_label
+task_name: MRIsCALabel
 nipype_name: MRIsCALabel
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mr_is_calc.yaml b/nipype-auto-conv/specs/mr_is_calc.yaml
@@ -28,7 +28,7 @@
 #     >>> example.cmdline # doctest: +SKIP
 #     'mris_calc -o lh.area.mid lh.area add lh.area.pial'
 #     
-task_name: mr_is_calc
+task_name: MRIsCalc
 nipype_name: MRIsCalc
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mr_is_combine.yaml b/nipype-auto-conv/specs/mr_is_combine.yaml
@@ -29,7 +29,7 @@
 #     'mris_convert --combinesurfs lh.pial rh.pial bh.pial'
 #     >>> mris.run()  # doctest: +SKIP
 #     
-task_name: mr_is_combine
+task_name: MRIsCombine
 nipype_name: MRIsCombine
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mr_is_convert.yaml b/nipype-auto-conv/specs/mr_is_convert.yaml
@@ -17,7 +17,7 @@
 #     >>> mris.inputs.out_datatype = 'gii'
 #     >>> mris.run() # doctest: +SKIP
 #     
-task_name: mr_is_convert
+task_name: MRIsConvert
 nipype_name: MRIsConvert
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mr_is_expand.yaml b/nipype-auto-conv/specs/mr_is_expand.yaml
@@ -20,7 +20,7 @@
 #     >>> mris_expand.cmdline
 #     'mris_expand -thickness lh.white 0.5 graymid'
 #     
-task_name: mr_is_expand
+task_name: MRIsExpand
 nipype_name: MRIsExpand
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mr_is_inflate.yaml b/nipype-auto-conv/specs/mr_is_inflate.yaml
@@ -17,7 +17,7 @@
 #     >>> inflate.cmdline # doctest: +SKIP
 #     'mris_inflate -no-save-sulc lh.pial lh.inflated'
 #     
-task_name: mr_is_inflate
+task_name: MRIsInflate
 nipype_name: MRIsInflate
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mri_convert.yaml b/nipype-auto-conv/specs/mri_convert.yaml
@@ -21,7 +21,7 @@
 #     'mri_convert --out_type mgz --input_volume structural.nii --output_volume outfile.mgz'
 # 
 #     
-task_name: mri_convert
+task_name: MRIConvert
 nipype_name: MRIConvert
 nipype_module: nipype.interfaces.freesurfer
 inputs:

diff --git a/nipype-auto-conv/specs/mri_coreg.yaml b/nipype-auto-conv/specs/mri_coreg.yaml
@@ -39,7 +39,7 @@
 #     >>> coreg.cmdline # doctest: +ELLIPSIS
 #     'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --sep 5 --mov moving1.nii --sd .'
 #     
-task_name: mri_coreg
+task_name: MRICoreg
 nipype_name: MRICoreg
 nipype_module: nipype.interfaces.freesurfer
 inputs: