From 817da914aa6fca9bb3744129d250812272c7f67b Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 2 Nov 2023 11:10:37 +1100 Subject: [PATCH 1/5] Reverted task names from snake case to pascal case --- .../specs/add_x_form_to_header.yaml | 2 +- nipype-auto-conv/specs/aparc_2_aseg.yaml | 2 +- nipype-auto-conv/specs/apas_2_aseg.yaml | 2 +- nipype-auto-conv/specs/apply_mask.yaml | 2 +- .../specs/apply_vol_transform.yaml | 2 +- nipype-auto-conv/specs/bb_register.yaml | 2 +- nipype-auto-conv/specs/binarize.yaml | 2 +- nipype-auto-conv/specs/ca_label.yaml | 2 +- nipype-auto-conv/specs/ca_normalize.yaml | 2 +- nipype-auto-conv/specs/ca_register.yaml | 2 +- .../specs/check_talairach_alignment.yaml | 2 +- nipype-auto-conv/specs/concatenate.yaml | 2 +- nipype-auto-conv/specs/concatenate_lta.yaml | 2 +- nipype-auto-conv/specs/contrast.yaml | 2 +- nipype-auto-conv/specs/curvature.yaml | 2 +- nipype-auto-conv/specs/curvature_stats.yaml | 2 +- nipype-auto-conv/specs/dicom_convert.yaml | 2 +- nipype-auto-conv/specs/edit_w_mwith_aseg.yaml | 2 +- nipype-auto-conv/specs/em_register.yaml | 2 +- nipype-auto-conv/specs/euler_number.yaml | 2 +- .../specs/extract_main_component.yaml | 2 +- nipype-auto-conv/specs/fit_ms_params.yaml | 2 +- nipype-auto-conv/specs/fix_topology.yaml | 2 +- .../specs/fuse_segmentations.yaml | 2 +- nipype-auto-conv/specs/glm_fit.yaml | 2 +- nipype-auto-conv/specs/gtm_seg.yaml | 2 +- nipype-auto-conv/specs/gtmpvc.yaml | 2 +- nipype-auto-conv/specs/jacobian.yaml | 2 +- nipype-auto-conv/specs/label_2_annot.yaml | 2 +- nipype-auto-conv/specs/label_2_label.yaml | 2 +- nipype-auto-conv/specs/label_2_vol.yaml | 2 +- .../specs/make_average_subject.yaml | 2 +- nipype-auto-conv/specs/make_surfaces.yaml | 2 +- .../specs/mni_bias_correction.yaml | 2 +- nipype-auto-conv/specs/mp_rto_mni305.yaml | 2 +- nipype-auto-conv/specs/mr_is_ca_label.yaml | 2 +- nipype-auto-conv/specs/mr_is_calc.yaml | 2 +- nipype-auto-conv/specs/mr_is_combine.yaml | 2 +- nipype-auto-conv/specs/mr_is_convert.yaml | 2 +- nipype-auto-conv/specs/mr_is_expand.yaml | 2 +- nipype-auto-conv/specs/mr_is_inflate.yaml | 2 +- nipype-auto-conv/specs/mri_convert.yaml | 2 +- nipype-auto-conv/specs/mri_coreg.yaml | 2 +- nipype-auto-conv/specs/mri_fill.yaml | 2 +- .../specs/mri_marching_cubes.yaml | 2 +- nipype-auto-conv/specs/mri_pretess.yaml | 2 +- nipype-auto-conv/specs/mri_tessellate.yaml | 2 +- nipype-auto-conv/specs/mris_preproc.yaml | 2 +- .../specs/mris_preproc_recon_all.yaml | 2 +- nipype-auto-conv/specs/ms__lda.yaml | 2 +- nipype-auto-conv/specs/normalize.yaml | 2 +- nipype-auto-conv/specs/one_sample_t_test.yaml | 2 +- nipype-auto-conv/specs/paint.yaml | 2 +- .../specs/parcellation_stats.yaml | 2 +- nipype-auto-conv/specs/parse_dicom_dir.yaml | 2 +- nipype-auto-conv/specs/recon_all.yaml | 128 +----------------- nipype-auto-conv/specs/register.yaml | 2 +- .../specs/register_av_ito_talairach.yaml | 2 +- .../specs/relabel_hypointensities.yaml | 2 +- .../specs/remove_intersection.yaml | 2 +- nipype-auto-conv/specs/remove_neck.yaml | 2 +- nipype-auto-conv/specs/resample.yaml | 2 +- nipype-auto-conv/specs/robust_register.yaml | 2 +- nipype-auto-conv/specs/robust_template.yaml | 8 +- nipype-auto-conv/specs/sample_to_surface.yaml | 2 +- nipype-auto-conv/specs/seg_stats.yaml | 2 +- .../specs/seg_stats_recon_all.yaml | 2 +- nipype-auto-conv/specs/segment_cc.yaml | 2 +- nipype-auto-conv/specs/segment_wm.yaml | 2 +- nipype-auto-conv/specs/smooth.yaml | 2 +- .../specs/smooth_tessellation.yaml | 2 +- nipype-auto-conv/specs/sphere.yaml | 2 +- nipype-auto-conv/specs/spherical_average.yaml | 2 +- .../specs/surface_2_vol_transform.yaml | 2 +- nipype-auto-conv/specs/surface_smooth.yaml | 2 +- nipype-auto-conv/specs/surface_snapshots.yaml | 2 +- nipype-auto-conv/specs/surface_transform.yaml | 2 +- nipype-auto-conv/specs/synthesize_flash.yaml | 2 +- nipype-auto-conv/specs/talairach_avi.yaml | 2 +- nipype-auto-conv/specs/talairach_qc.yaml | 2 +- nipype-auto-conv/specs/tkregister_2.yaml | 2 +- nipype-auto-conv/specs/unpack_sdicom_dir.yaml | 2 +- nipype-auto-conv/specs/volume_mask.yaml | 2 +- .../specs/watershed_skull_strip.yaml | 2 +- 84 files changed, 89 insertions(+), 211 deletions(-) diff --git a/nipype-auto-conv/specs/add_x_form_to_header.yaml b/nipype-auto-conv/specs/add_x_form_to_header.yaml index 2399ea6..b7d9856 100644 --- 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 index 928ab21..36713f6 100644 --- 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 index cc0d6e2..2e323ad 100644 --- 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 index e17e003..893825c 100644 --- 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 index fa5f3e5..6da9b21 100644 --- 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 index 8d21eb9..5173b17 100644 --- 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 index e515e71..586affe 100644 --- 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 index 6a7b782..dda0348 100644 --- 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 index a9c4459..f4a70c4 100644 --- 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 index d45e393..bb38906 100644 --- 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 index 560e7ff..f883729 100644 --- 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 index 6d1de57..e03a17b 100644 --- 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 index 8a253bc..fcfcb12 100644 --- 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 index e676eab..3fb0bfc 100644 --- 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 index 241c820..c7a38d6 100644 --- 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 index f67ee0d..2f5db66 100644 --- 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 index e3dd676..b717d98 100644 --- 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 index ec928ae..0746851 100644 --- 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 index 96cfeff..6f27d37 100644 --- 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 index 3ff8920..51b15ba 100644 --- 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 index 81005fc..59317fe 100644 --- 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 index cf6494d..e6a757b 100644 --- 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 index f4a2a24..90a4388 100644 --- 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 index fd4f366..e6c7ea0 100644 --- 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 index b29ad11..0061edd 100644 --- 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 index 093eabc..699ae60 100644 --- 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 index 071aab6..9a20364 100644 --- 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 index e79ae7e..73867ac 100644 --- 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 index d63c482..45b7ee8 100644 --- 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 index 29fe500..cf0ad53 100644 --- 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 index bcd6b79..868e87c 100644 --- 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 index 036dcd2..9451524 100644 --- 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 index 4733223..b052dd2 100644 --- 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 index 2da03cb..2b4a841 100644 --- 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 index 8a32759..167e59a 100644 --- 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 index 64333f5..c9ca687 100644 --- 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 index 2e245e0..d44dd0b 100644 --- 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 index cadd96e..23f42b0 100644 --- 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 index 39c9a8f..70184f1 100644 --- 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 index 7aa7bab..fc42f21 100644 --- 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 index c08bfbd..8f35dcd 100644 --- 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 index cdf4339..bb209ea 100644 --- 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 index ae85b80..20b9d7b 100644 --- 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: diff --git a/nipype-auto-conv/specs/mri_fill.yaml b/nipype-auto-conv/specs/mri_fill.yaml index 7ecf964..cbb0b2b 100644 --- a/nipype-auto-conv/specs/mri_fill.yaml +++ b/nipype-auto-conv/specs/mri_fill.yaml @@ -18,7 +18,7 @@ # >>> fill.cmdline # doctest: +SKIP # 'mri_fill wm.mgz filled.mgz' # -task_name: mri_fill +task_name: MRIFill nipype_name: MRIFill nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/mri_marching_cubes.yaml b/nipype-auto-conv/specs/mri_marching_cubes.yaml index 250c65a..ec33151 100644 --- a/nipype-auto-conv/specs/mri_marching_cubes.yaml +++ b/nipype-auto-conv/specs/mri_marching_cubes.yaml @@ -18,7 +18,7 @@ # >>> mc.inputs.out_file = 'lh.hippocampus' # >>> mc.run() # doctest: +SKIP # -task_name: mri_marching_cubes +task_name: MRIMarchingCubes nipype_name: MRIMarchingCubes nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/mri_pretess.yaml b/nipype-auto-conv/specs/mri_pretess.yaml index a2a6c18..452754c 100644 --- a/nipype-auto-conv/specs/mri_pretess.yaml +++ b/nipype-auto-conv/specs/mri_pretess.yaml @@ -24,7 +24,7 @@ # >>> pretess.run() # doctest: +SKIP # # -task_name: mri_pretess +task_name: MRIPretess nipype_name: MRIPretess nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/mri_tessellate.yaml b/nipype-auto-conv/specs/mri_tessellate.yaml index 54af8f2..9fccf07 100644 --- a/nipype-auto-conv/specs/mri_tessellate.yaml +++ b/nipype-auto-conv/specs/mri_tessellate.yaml @@ -18,7 +18,7 @@ # >>> tess.inputs.out_file = 'lh.hippocampus' # >>> tess.run() # doctest: +SKIP # -task_name: mri_tessellate +task_name: MRITessellate nipype_name: MRITessellate nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/mris_preproc.yaml b/nipype-auto-conv/specs/mris_preproc.yaml index 7eab5db..19d18e0 100644 --- a/nipype-auto-conv/specs/mris_preproc.yaml +++ b/nipype-auto-conv/specs/mris_preproc.yaml @@ -19,7 +19,7 @@ # 'mris_preproc --hemi lh --out concatenated_file.mgz --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat' # # -task_name: mris_preproc +task_name: MRISPreproc nipype_name: MRISPreproc nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/mris_preproc_recon_all.yaml b/nipype-auto-conv/specs/mris_preproc_recon_all.yaml index 5ed7c59..94f8493 100644 --- a/nipype-auto-conv/specs/mris_preproc_recon_all.yaml +++ b/nipype-auto-conv/specs/mris_preproc_recon_all.yaml @@ -18,7 +18,7 @@ # 'mris_preproc --hemi lh --out concatenated_file.mgz --s subject_id --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat' # # -task_name: mris_preproc_recon_all +task_name: MRISPreprocReconAll nipype_name: MRISPreprocReconAll nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/ms__lda.yaml b/nipype-auto-conv/specs/ms__lda.yaml index 0762c32..3c8f28b 100644 --- a/nipype-auto-conv/specs/ms__lda.yaml +++ b/nipype-auto-conv/specs/ms__lda.yaml @@ -17,7 +17,7 @@ # 'mri_ms_LDA -conform -label label.mgz -lda 2 3 -shift 1 -W -synth synth_out.mgz -weight weights.txt FLASH1.mgz FLASH2.mgz FLASH3.mgz' # # -task_name: ms__lda +task_name: MS_LDA nipype_name: MS_LDA nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/normalize.yaml b/nipype-auto-conv/specs/normalize.yaml index d18e50e..686b041 100644 --- a/nipype-auto-conv/specs/normalize.yaml +++ b/nipype-auto-conv/specs/normalize.yaml @@ -19,7 +19,7 @@ # >>> normalize.cmdline # 'mri_normalize -g 1 T1.mgz T1_norm.mgz' # -task_name: normalize +task_name: Normalize nipype_name: Normalize nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/one_sample_t_test.yaml b/nipype-auto-conv/specs/one_sample_t_test.yaml index 13e4fc5..5296c9e 100644 --- a/nipype-auto-conv/specs/one_sample_t_test.yaml +++ b/nipype-auto-conv/specs/one_sample_t_test.yaml @@ -6,7 +6,7 @@ # Docs # ---- # -task_name: one_sample_t_test +task_name: OneSampleTTest nipype_name: OneSampleTTest nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/paint.yaml b/nipype-auto-conv/specs/paint.yaml index 35068e2..e7d84ee 100644 --- a/nipype-auto-conv/specs/paint.yaml +++ b/nipype-auto-conv/specs/paint.yaml @@ -23,7 +23,7 @@ # >>> paint.cmdline # 'mrisp_paint -a 5 aseg.mgz lh.pial lh.avg_curv' # -task_name: paint +task_name: Paint nipype_name: Paint nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/parcellation_stats.yaml b/nipype-auto-conv/specs/parcellation_stats.yaml index a4d7eed..603a40b 100644 --- a/nipype-auto-conv/specs/parcellation_stats.yaml +++ b/nipype-auto-conv/specs/parcellation_stats.yaml @@ -31,7 +31,7 @@ # >>> parcstats.cmdline # doctest: +SKIP # 'mris_anatomical_stats -c test.ctab -f lh.test.stats 10335 lh white' # -task_name: parcellation_stats +task_name: ParcellationStats nipype_name: ParcellationStats nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/parse_dicom_dir.yaml b/nipype-auto-conv/specs/parse_dicom_dir.yaml index b9a94d3..9d6bc9c 100644 --- a/nipype-auto-conv/specs/parse_dicom_dir.yaml +++ b/nipype-auto-conv/specs/parse_dicom_dir.yaml @@ -19,7 +19,7 @@ # 'mri_parse_sdcmdir --d . --o dicominfo.txt --sortbyrun --summarize' # # -task_name: parse_dicom_dir +task_name: ParseDICOMDir nipype_name: ParseDICOMDir nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/recon_all.yaml b/nipype-auto-conv/specs/recon_all.yaml index 1bcbe9b..fcbda1e 100644 --- a/nipype-auto-conv/specs/recon_all.yaml +++ b/nipype-auto-conv/specs/recon_all.yaml @@ -16,7 +16,7 @@ # >>> reconall.inputs.subject_id = 'foo' # >>> reconall.inputs.directive = 'all' # >>> reconall.inputs.subjects_dir = '.' -# >>> reconall.inputs.T1_files = ['structural.nii'] +# >>> reconall.inputs.T1_files = 'structural.nii' # >>> reconall.cmdline # 'recon-all -all -i structural.nii -subjid foo -sd .' # >>> reconall.inputs.flags = "-qcache" @@ -46,7 +46,7 @@ # >>> reconall_subfields.inputs.subject_id = 'foo' # >>> reconall_subfields.inputs.directive = 'all' # >>> reconall_subfields.inputs.subjects_dir = '.' -# >>> reconall_subfields.inputs.T1_files = ['structural.nii'] +# >>> reconall_subfields.inputs.T1_files = 'structural.nii' # >>> reconall_subfields.inputs.hippocampal_subfields_T1 = True # >>> reconall_subfields.cmdline # 'recon-all -all -i structural.nii -hippocampal-subfields-T1 -subjid foo -sd .' @@ -57,26 +57,8 @@ # >>> reconall_subfields.inputs.hippocampal_subfields_T1 = False # >>> reconall_subfields.cmdline # 'recon-all -all -i structural.nii -hippocampal-subfields-T2 structural.nii test -subjid foo -sd .' -# -# Base template creation for longitudinal pipeline: -# >>> baserecon = ReconAll() -# >>> baserecon.inputs.base_template_id = 'sub-template' -# >>> baserecon.inputs.base_timepoint_ids = ['ses-1','ses-2'] -# >>> baserecon.inputs.directive = 'all' -# >>> baserecon.inputs.subjects_dir = '.' -# >>> baserecon.cmdline -# 'recon-all -all -base sub-template -base-tp ses-1 -base-tp ses-2 -sd .' -# -# Longitudinal timepoint run: -# >>> longrecon = ReconAll() -# >>> longrecon.inputs.longitudinal_timepoint_id = 'ses-1' -# >>> longrecon.inputs.longitudinal_template_id = 'sub-template' -# >>> longrecon.inputs.directive = 'all' -# >>> longrecon.inputs.subjects_dir = '.' -# >>> longrecon.cmdline -# 'recon-all -all -long ses-1 sub-template -sd .' # -task_name: recon_all +task_name: ReconAll nipype_name: ReconAll nipype_module: nipype.interfaces.freesurfer inputs: @@ -100,8 +82,6 @@ inputs: # type=file|default=: Set parameters using expert file flags: generic/file+list-of # type=inputmultiobject|default=[]: additional parameters - base_timepoint_ids: generic/file+list-of - # type=inputmultiobject|default=[]: processed timepoint to use in template metadata: # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1) outputs: @@ -193,14 +173,6 @@ tests: # type=directory|default=: path to subjects directory flags: # type=inputmultiobject|default=[]: additional parameters - base_template_id: - # type=str|default='': base template id - base_timepoint_ids: - # type=inputmultiobject|default=[]: processed timepoint to use in template - longitudinal_timepoint_id: - # type=str|default='': longitudinal session/timepoint id - longitudinal_template_id: - # type=str|default='': longitudinal base template id talairach: # type=str|default='': Flags to pass to talairach commands mri_normalize: @@ -376,60 +348,6 @@ tests: xfail: true # bool - whether the unittest is expected to fail or not. Set to false # when you are satisfied with the edits you have made to this file -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - base_template_id: '"sub-template"' - # type=str|default='': base template id - base_timepoint_ids: - # type=inputmultiobject|default=[]: processed timepoint to use in template - directive: '"all"' - # type=enum|default='all'|allowed['all','autorecon-hemi','autorecon-pial','autorecon1','autorecon2','autorecon2-cp','autorecon2-inflate1','autorecon2-perhemi','autorecon2-volonly','autorecon2-wm','autorecon3','autorecon3-T2pial','localGI','qcache']: process directive - subjects_dir: '"."' - # type=directory: Freesurfer subjects directory. - # type=directory|default=: path to subjects directory - imports: - # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file -- inputs: - # dict[str, str] - values to provide to inputs fields in the task initialisation - # (if not specified, will try to choose a sensible value) - longitudinal_timepoint_id: '"ses-1"' - # type=str|default='': longitudinal session/timepoint id - longitudinal_template_id: '"sub-template"' - # type=str|default='': longitudinal base template id - directive: '"all"' - # type=enum|default='all'|allowed['all','autorecon-hemi','autorecon-pial','autorecon1','autorecon2','autorecon2-cp','autorecon2-inflate1','autorecon2-perhemi','autorecon2-volonly','autorecon2-wm','autorecon3','autorecon3-T2pial','localGI','qcache']: process directive - subjects_dir: '"."' - # type=directory: Freesurfer subjects directory. - # type=directory|default=: path to subjects directory - imports: - # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - expected_outputs: - # dict[str, str] - expected values for selected outputs, noting that tests will typically - # be terminated before they complete for time-saving reasons, and therefore - # these values will be ignored, when running in CI - timeout: 10 - # int - the value to set for the timeout in the generated test, - # after which the test will be considered to have been initialised - # successfully. Set to 0 to disable the timeout (warning, this could - # lead to the unittests taking a very long time to complete) - xfail: true - # bool - whether the unittest is expected to fail or not. Set to false - # when you are satisfied with the edits you have made to this file doctests: - cmdline: recon-all -all -i structural.nii -cw256 -qcache -subjid foo -sd . # str - the expected cmdline output @@ -507,43 +425,3 @@ doctests: # consisting of 'module', 'name', and optionally 'alias' keys directive: # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS -- cmdline: recon-all -all -base sub-template -base-tp ses-1 -base-tp ses-2 -sd . - # str - the expected cmdline output - inputs: - # dict[str, str] - name-value pairs for inputs to be provided to the doctest. - # If the field is of file-format type and the value is None, then the - # '.mock()' method of the corresponding class is used instead. - base_template_id: '"sub-template"' - # type=str|default='': base template id - base_timepoint_ids: - # type=inputmultiobject|default=[]: processed timepoint to use in template - directive: '"all"' - # type=enum|default='all'|allowed['all','autorecon-hemi','autorecon-pial','autorecon1','autorecon2','autorecon2-cp','autorecon2-inflate1','autorecon2-perhemi','autorecon2-volonly','autorecon2-wm','autorecon3','autorecon3-T2pial','localGI','qcache']: process directive - subjects_dir: '"."' - # type=directory: Freesurfer subjects directory. - # type=directory|default=: path to subjects directory - imports: - # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - directive: - # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS -- cmdline: recon-all -all -long ses-1 sub-template -sd . - # str - the expected cmdline output - inputs: - # dict[str, str] - name-value pairs for inputs to be provided to the doctest. - # If the field is of file-format type and the value is None, then the - # '.mock()' method of the corresponding class is used instead. - longitudinal_timepoint_id: '"ses-1"' - # type=str|default='': longitudinal session/timepoint id - longitudinal_template_id: '"sub-template"' - # type=str|default='': longitudinal base template id - directive: '"all"' - # type=enum|default='all'|allowed['all','autorecon-hemi','autorecon-pial','autorecon1','autorecon2','autorecon2-cp','autorecon2-inflate1','autorecon2-perhemi','autorecon2-volonly','autorecon2-wm','autorecon3','autorecon3-T2pial','localGI','qcache']: process directive - subjects_dir: '"."' - # type=directory: Freesurfer subjects directory. - # type=directory|default=: path to subjects directory - imports: - # list[nipype2pydra.task.importstatement] - list import statements required by the test, with each list item - # consisting of 'module', 'name', and optionally 'alias' keys - directive: - # str - any doctest directive to place on the cmdline call, e.g. # doctest: +ELLIPSIS diff --git a/nipype-auto-conv/specs/register.yaml b/nipype-auto-conv/specs/register.yaml index 98d5582..80f3618 100644 --- a/nipype-auto-conv/specs/register.yaml +++ b/nipype-auto-conv/specs/register.yaml @@ -20,7 +20,7 @@ # >>> register.cmdline # 'mris_register -curv lh.pial aseg.mgz lh.pial.reg' # -task_name: register +task_name: Register nipype_name: Register nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/register_av_ito_talairach.yaml b/nipype-auto-conv/specs/register_av_ito_talairach.yaml index 4473666..30d3e81 100644 --- a/nipype-auto-conv/specs/register_av_ito_talairach.yaml +++ b/nipype-auto-conv/specs/register_av_ito_talairach.yaml @@ -30,7 +30,7 @@ # # >>> register.run() # doctest: +SKIP # -task_name: register_av_ito_talairach +task_name: RegisterAVItoTalairach nipype_name: RegisterAVItoTalairach nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/relabel_hypointensities.yaml b/nipype-auto-conv/specs/relabel_hypointensities.yaml index 471ecee..8d4e170 100644 --- a/nipype-auto-conv/specs/relabel_hypointensities.yaml +++ b/nipype-auto-conv/specs/relabel_hypointensities.yaml @@ -19,7 +19,7 @@ # >>> relabelhypos.cmdline # 'mri_relabel_hypointensities aseg.mgz . aseg.hypos.mgz' # -task_name: relabel_hypointensities +task_name: RelabelHypointensities nipype_name: RelabelHypointensities nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/remove_intersection.yaml b/nipype-auto-conv/specs/remove_intersection.yaml index f619b34..9d22a4b 100644 --- a/nipype-auto-conv/specs/remove_intersection.yaml +++ b/nipype-auto-conv/specs/remove_intersection.yaml @@ -16,7 +16,7 @@ # >>> ri.cmdline # 'mris_remove_intersection lh.pial lh.pial' # -task_name: remove_intersection +task_name: RemoveIntersection nipype_name: RemoveIntersection nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/remove_neck.yaml b/nipype-auto-conv/specs/remove_neck.yaml index 553401c..c3e89bb 100644 --- a/nipype-auto-conv/specs/remove_neck.yaml +++ b/nipype-auto-conv/specs/remove_neck.yaml @@ -19,7 +19,7 @@ # >>> remove_neck.cmdline # 'mri_remove_neck norm.mgz trans.mat trans.mat norm_noneck.mgz' # -task_name: remove_neck +task_name: RemoveNeck nipype_name: RemoveNeck nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/resample.yaml b/nipype-auto-conv/specs/resample.yaml index 90e4839..083d8f5 100644 --- a/nipype-auto-conv/specs/resample.yaml +++ b/nipype-auto-conv/specs/resample.yaml @@ -19,7 +19,7 @@ # 'mri_convert -vs 2.10 2.10 2.10 -i structural.nii -o resampled.nii' # # -task_name: resample +task_name: Resample nipype_name: Resample nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/robust_register.yaml b/nipype-auto-conv/specs/robust_register.yaml index 2ec5a15..cea912d 100644 --- a/nipype-auto-conv/specs/robust_register.yaml +++ b/nipype-auto-conv/specs/robust_register.yaml @@ -25,7 +25,7 @@ # Consistent Registration: A Robust Approach. Neuroimage 53(4) 1181-96. # # -task_name: robust_register +task_name: RobustRegister nipype_name: RobustRegister nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/robust_template.yaml b/nipype-auto-conv/specs/robust_template.yaml index 74c9eba..9ebe5dc 100644 --- a/nipype-auto-conv/specs/robust_template.yaml +++ b/nipype-auto-conv/specs/robust_template.yaml @@ -43,7 +43,7 @@ # [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template] # # -task_name: robust_template +task_name: RobustTemplate nipype_name: RobustTemplate nipype_module: nipype.interfaces.freesurfer inputs: @@ -115,7 +115,7 @@ tests: average_metric: # type=enum|default='median'|allowed['mean','median']: construct template from: 0 Mean, 1 Median (default) initial_timepoint: - # type=int|default=0: use TP# for special init (default random), 0: no init + # type=int|default=0: use TP# for spacial init (default random), 0: no init fixed_timepoint: # type=bool|default=False: map everything to init TP# (init TP is not resampled) no_iteration: @@ -157,7 +157,7 @@ tests: average_metric: '"mean"' # type=enum|default='median'|allowed['mean','median']: construct template from: 0 Mean, 1 Median (default) initial_timepoint: '1' - # type=int|default=0: use TP# for special init (default random), 0: no init + # type=int|default=0: use TP# for spacial init (default random), 0: no init fixed_timepoint: 'True' # type=bool|default=False: map everything to init TP# (init TP is not resampled) no_iteration: 'True' @@ -244,7 +244,7 @@ doctests: average_metric: '"mean"' # type=enum|default='median'|allowed['mean','median']: construct template from: 0 Mean, 1 Median (default) initial_timepoint: '1' - # type=int|default=0: use TP# for special init (default random), 0: no init + # type=int|default=0: use TP# for spacial init (default random), 0: no init fixed_timepoint: 'True' # type=bool|default=False: map everything to init TP# (init TP is not resampled) no_iteration: 'True' diff --git a/nipype-auto-conv/specs/sample_to_surface.yaml b/nipype-auto-conv/specs/sample_to_surface.yaml index 6de576d..352ff07 100644 --- a/nipype-auto-conv/specs/sample_to_surface.yaml +++ b/nipype-auto-conv/specs/sample_to_surface.yaml @@ -34,7 +34,7 @@ # >>> res = sampler.run() # doctest: +SKIP # # -task_name: sample_to_surface +task_name: SampleToSurface nipype_name: SampleToSurface nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/seg_stats.yaml b/nipype-auto-conv/specs/seg_stats.yaml index 7553a70..a25079f 100644 --- a/nipype-auto-conv/specs/seg_stats.yaml +++ b/nipype-auto-conv/specs/seg_stats.yaml @@ -20,7 +20,7 @@ # 'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --i functional.nii --sum ./summary.stats' # # -task_name: seg_stats +task_name: SegStats nipype_name: SegStats nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/seg_stats_recon_all.yaml b/nipype-auto-conv/specs/seg_stats_recon_all.yaml index 68871b6..7f7074a 100644 --- a/nipype-auto-conv/specs/seg_stats_recon_all.yaml +++ b/nipype-auto-conv/specs/seg_stats_recon_all.yaml @@ -42,7 +42,7 @@ # 'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --brain-vol-from-seg --surf-ctx-vol --empty --etiv --euler --excl-ctxgmwm --excludeid 0 --subcortgray --subject 10335 --supratent --totalgray --surf-wm-vol --sum ./summary.stats' # # -task_name: seg_stats_recon_all +task_name: SegStatsReconAll nipype_name: SegStatsReconAll nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/segment_cc.yaml b/nipype-auto-conv/specs/segment_cc.yaml index 9516c8f..5a826c9 100644 --- a/nipype-auto-conv/specs/segment_cc.yaml +++ b/nipype-auto-conv/specs/segment_cc.yaml @@ -26,7 +26,7 @@ # >>> SegmentCC_node.cmdline # 'mri_cc -aseg aseg.mgz -o aseg.auto.mgz -lta cc.lta test' # -task_name: segment_cc +task_name: SegmentCC nipype_name: SegmentCC nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/segment_wm.yaml b/nipype-auto-conv/specs/segment_wm.yaml index c555368..ed11dc6 100644 --- a/nipype-auto-conv/specs/segment_wm.yaml +++ b/nipype-auto-conv/specs/segment_wm.yaml @@ -20,7 +20,7 @@ # >>> SegmentWM_node.cmdline # 'mri_segment norm.mgz wm.seg.mgz' # -task_name: segment_wm +task_name: SegmentWM nipype_name: SegmentWM nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/smooth.yaml b/nipype-auto-conv/specs/smooth.yaml index 6c3ce0f..b4944db 100644 --- a/nipype-auto-conv/specs/smooth.yaml +++ b/nipype-auto-conv/specs/smooth.yaml @@ -25,7 +25,7 @@ # 'mris_volsmooth --i functional.nii --reg register.dat --o foo_out.nii --fwhm 10.000000 --vol-fwhm 6.000000' # # -task_name: smooth +task_name: Smooth nipype_name: Smooth nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/smooth_tessellation.yaml b/nipype-auto-conv/specs/smooth_tessellation.yaml index fa20118..84f1514 100644 --- a/nipype-auto-conv/specs/smooth_tessellation.yaml +++ b/nipype-auto-conv/specs/smooth_tessellation.yaml @@ -21,7 +21,7 @@ # >>> smooth.run() # doctest: +SKIP # # -task_name: smooth_tessellation +task_name: SmoothTessellation nipype_name: SmoothTessellation nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/sphere.yaml b/nipype-auto-conv/specs/sphere.yaml index 6426f1a..87b33bf 100644 --- a/nipype-auto-conv/specs/sphere.yaml +++ b/nipype-auto-conv/specs/sphere.yaml @@ -16,7 +16,7 @@ # >>> sphere.cmdline # 'mris_sphere lh.pial lh.sphere' # -task_name: sphere +task_name: Sphere nipype_name: Sphere nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/spherical_average.yaml b/nipype-auto-conv/specs/spherical_average.yaml index 2b752d3..303748c 100644 --- a/nipype-auto-conv/specs/spherical_average.yaml +++ b/nipype-auto-conv/specs/spherical_average.yaml @@ -25,7 +25,7 @@ # 'mris_spherical_average -erode 2 -o 10335 -t 5.0 label lh.entorhinal lh pial . test.out' # # -task_name: spherical_average +task_name: SphericalAverage nipype_name: SphericalAverage nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/surface_2_vol_transform.yaml b/nipype-auto-conv/specs/surface_2_vol_transform.yaml index 6b57c75..3d9d5b6 100644 --- a/nipype-auto-conv/specs/surface_2_vol_transform.yaml +++ b/nipype-auto-conv/specs/surface_2_vol_transform.yaml @@ -22,7 +22,7 @@ # >>> res = xfm2vol.run()# doctest: +SKIP # # -task_name: surface_2_vol_transform +task_name: Surface2VolTransform nipype_name: Surface2VolTransform nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/surface_smooth.yaml b/nipype-auto-conv/specs/surface_smooth.yaml index 5abf2e3..e4c976c 100644 --- a/nipype-auto-conv/specs/surface_smooth.yaml +++ b/nipype-auto-conv/specs/surface_smooth.yaml @@ -31,7 +31,7 @@ # >>> smoother.run() # doctest: +SKIP # # -task_name: surface_smooth +task_name: SurfaceSmooth nipype_name: SurfaceSmooth nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/surface_snapshots.yaml b/nipype-auto-conv/specs/surface_snapshots.yaml index 1eccc27..9173d08 100644 --- a/nipype-auto-conv/specs/surface_snapshots.yaml +++ b/nipype-auto-conv/specs/surface_snapshots.yaml @@ -30,7 +30,7 @@ # >>> res = shots.run() # doctest: +SKIP # # -task_name: surface_snapshots +task_name: SurfaceSnapshots nipype_name: SurfaceSnapshots nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/surface_transform.yaml b/nipype-auto-conv/specs/surface_transform.yaml index 5ef2fb9..c22e0be 100644 --- a/nipype-auto-conv/specs/surface_transform.yaml +++ b/nipype-auto-conv/specs/surface_transform.yaml @@ -23,7 +23,7 @@ # >>> sxfm.run() # doctest: +SKIP # # -task_name: surface_transform +task_name: SurfaceTransform nipype_name: SurfaceTransform nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/synthesize_flash.yaml b/nipype-auto-conv/specs/synthesize_flash.yaml index 6e5ad1a..17ebc71 100644 --- a/nipype-auto-conv/specs/synthesize_flash.yaml +++ b/nipype-auto-conv/specs/synthesize_flash.yaml @@ -18,7 +18,7 @@ # 'mri_synthesize 20.00 30.00 3.000 T1.mgz PD.mgz flash_30syn.mgz' # # -task_name: synthesize_flash +task_name: SynthesizeFLASH nipype_name: SynthesizeFLASH nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/talairach_avi.yaml b/nipype-auto-conv/specs/talairach_avi.yaml index b0ef977..0be75e5 100644 --- a/nipype-auto-conv/specs/talairach_avi.yaml +++ b/nipype-auto-conv/specs/talairach_avi.yaml @@ -24,7 +24,7 @@ # # >>> example.run() # doctest: +SKIP # -task_name: talairach_avi +task_name: TalairachAVI nipype_name: TalairachAVI nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/talairach_qc.yaml b/nipype-auto-conv/specs/talairach_qc.yaml index e7716c4..718ff8b 100644 --- a/nipype-auto-conv/specs/talairach_qc.yaml +++ b/nipype-auto-conv/specs/talairach_qc.yaml @@ -15,7 +15,7 @@ # >>> qc.cmdline # 'tal_QC_AZS dirs.txt' # -task_name: talairach_qc +task_name: TalairachQC nipype_name: TalairachQC nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/tkregister_2.yaml b/nipype-auto-conv/specs/tkregister_2.yaml index feaf6cc..7c6c5a3 100644 --- a/nipype-auto-conv/specs/tkregister_2.yaml +++ b/nipype-auto-conv/specs/tkregister_2.yaml @@ -35,7 +35,7 @@ # 'tkregister2 --fsl flirt.mat --mov epi.nii --noedit --reg register.dat' # >>> tk2.run() # doctest: +SKIP # -task_name: tkregister_2 +task_name: Tkregister2 nipype_name: Tkregister2 nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/unpack_sdicom_dir.yaml b/nipype-auto-conv/specs/unpack_sdicom_dir.yaml index 1cd4d3f..bd5a0cc 100644 --- a/nipype-auto-conv/specs/unpack_sdicom_dir.yaml +++ b/nipype-auto-conv/specs/unpack_sdicom_dir.yaml @@ -22,7 +22,7 @@ # >>> unpack.cmdline # 'unpacksdcmdir -generic -targ . -run 5 mprage nii struct -src .' # -task_name: unpack_sdicom_dir +task_name: UnpackSDICOMDir nipype_name: UnpackSDICOMDir nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/volume_mask.yaml b/nipype-auto-conv/specs/volume_mask.yaml index 5c5f6f2..e1a99b6 100644 --- a/nipype-auto-conv/specs/volume_mask.yaml +++ b/nipype-auto-conv/specs/volume_mask.yaml @@ -31,7 +31,7 @@ # >>> volmask.cmdline # 'mris_volmask --label_left_ribbon 3 --label_left_white 2 --label_right_ribbon 42 --label_right_white 41 --save_ribbon 10335' # -task_name: volume_mask +task_name: VolumeMask nipype_name: VolumeMask nipype_module: nipype.interfaces.freesurfer inputs: diff --git a/nipype-auto-conv/specs/watershed_skull_strip.yaml b/nipype-auto-conv/specs/watershed_skull_strip.yaml index f9bf3d7..74adaeb 100644 --- a/nipype-auto-conv/specs/watershed_skull_strip.yaml +++ b/nipype-auto-conv/specs/watershed_skull_strip.yaml @@ -29,7 +29,7 @@ # >>> skullstrip.cmdline # 'mri_watershed -T1 transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz' # -task_name: watershed_skull_strip +task_name: WatershedSkullStrip nipype_name: WatershedSkullStrip nipype_module: nipype.interfaces.freesurfer inputs: From 39c02ffa1e8bf001710b1583cd955e770a4d6872 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 2 Nov 2023 11:14:06 +1100 Subject: [PATCH 2/5] put github workflows inside the right directory --- {workflows => .github/workflows}/pythonpackage.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {workflows => .github/workflows}/pythonpackage.yaml (100%) diff --git a/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml similarity index 100% rename from workflows/pythonpackage.yaml rename to .github/workflows/pythonpackage.yaml From 6ae2103a61bbf64b2e927f98acdb93338b9adafc Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 2 Nov 2023 12:37:51 +1100 Subject: [PATCH 3/5] added debugging statement to github workflow --- .github/workflows/pythonpackage.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml index 7d0c02c..fbbfaca 100644 --- a/.github/workflows/pythonpackage.yaml +++ b/.github/workflows/pythonpackage.yaml @@ -93,6 +93,10 @@ jobs: with: name: converted-nipype path: pydra/tasks/freesurfer/auto + - name: Check directory structure + run: | + apt install tree + tree . - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: From 348d5dba6002d85833264bd6d633bbeb6da5e698 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 2 Nov 2023 12:40:56 +1100 Subject: [PATCH 4/5] debugged directory structure check --- .github/workflows/pythonpackage.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml index fbbfaca..33c5b35 100644 --- a/.github/workflows/pythonpackage.yaml +++ b/.github/workflows/pythonpackage.yaml @@ -95,7 +95,7 @@ jobs: path: pydra/tasks/freesurfer/auto - name: Check directory structure run: | - apt install tree + sudo apt install tree tree . - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 From e1853b769e8c600b369ea5c815a5f208d3d8ec00 Mon Sep 17 00:00:00 2001 From: Tom Close Date: Thu, 2 Nov 2023 16:29:43 +1100 Subject: [PATCH 5/5] raise other import errors when attempting to import nipype version --- pydra/tasks/freesurfer/__init__.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/pydra/tasks/freesurfer/__init__.py b/pydra/tasks/freesurfer/__init__.py index 5dbe80c..0185301 100644 --- a/pydra/tasks/freesurfer/__init__.py +++ b/pydra/tasks/freesurfer/__init__.py @@ -21,11 +21,14 @@ try: from .auto._version import nipype_version, nipype2pydra_version except ImportError: - warn( - "Nipype interfaces haven't been automatically converted from their specs in " - f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` " - "to generated the converted Nipype interfaces in pydra.tasks.freesurfer.auto" - ) + if "No module named pydra.tasks.freesurfer.auto._version": + warn( + "Nipype interfaces haven't been automatically converted from their specs in " + f"`nipype-auto-conv`. Please run `{str(pkg_path / 'nipype-auto-conv' / 'generate')}` " + "to generated the converted Nipype interfaces in pydra.tasks.freesurfer.auto" + ) + else: + raise else: n_ver = nipype_version.replace(".", "_") n2p_ver = nipype2pydra_version.replace(".", "_")