@@ -351,20 +351,28 @@ def crop_and_move_datasets(subject_id, subjects_dir, fs_dir, parcellation_name,
351
351
mri_cmd = 'mri_convert -rl "%s" -rt nearest "%s" -nc "%s"' % (orig , d [0 ], d [1 ])
352
352
runCmd ( mri_cmd ,log )
353
353
354
+
354
355
class ParcellateInputSpec (BaseInterfaceInputSpec ):
355
356
subject_id = traits .String (mandatory = True , desc = 'Subject ID' )
356
- parcellation_name = traits .Enum ('scale500' , ['scale33' , 'scale60' , 'scale125' , 'scale250' ,'scale500' ], usedefault = True )
357
+ parcellation_name = traits .Enum ('scale500' , ['scale33' , 'scale60' , 'scale125' , 'scale250' , 'scale500' ], usedefault = True )
357
358
freesurfer_dir = Directory (desc = 'Freesurfer main directory' )
358
359
subjects_dir = Directory (desc = 'Freesurfer main directory' )
359
- out_roi_file = File (genfile = True , desc = 'Region of Interest file for connectivity mapping' )
360
+ out_roi_file = File (genfile = True , desc = 'Region of Interest file for connectivity mapping' )
361
+
360
362
361
363
class ParcellateOutputSpec (TraitedSpec ):
362
- roi_file = File (desc = 'Region of Interest file for connectivity mapping' )
364
+ roi_file = File (desc = 'Region of Interest file for connectivity mapping' ,
365
+ exists = True )
363
366
white_matter_mask_file = File (desc = 'White matter mask file' )
364
- cc_unknown_file = File (desc = 'Image file with regions labelled as unknown cortical structures' )
365
- ribbon_file = File (desc = 'Image file detailing the cortical ribbon' )
366
- aseg_file = File (desc = 'Automated segmentation file converted from Freesurfer "subjects" directory' )
367
- roi_file_in_structural_space = File (desc = 'ROI image resliced to the dimensions of the original structural image' )
367
+ cc_unknown_file = File (desc = 'Image file with regions labelled as unknown cortical structures' ,
368
+ exists = True )
369
+ ribbon_file = File (desc = 'Image file detailing the cortical ribbon' ,
370
+ exists = True )
371
+ aseg_file = File (desc = 'Automated segmentation file converted from Freesurfer "subjects" directory' ,
372
+ exists = True )
373
+ roi_file_in_structural_space = File (desc = 'ROI image resliced to the dimensions of the original structural image' ,
374
+ exists = True )
375
+
368
376
369
377
class Parcellate (BaseInterface ):
370
378
"""Subdivides segmented ROI file into smaller subregions
0 commit comments