fix: compcor option

Author: akeshavan

bips/workflows/scripts/u0a14c5b5899911e1bca80023dfa375f2/base.py

@@ -180,7 +180,8 @@ def create_prep(name='preproc'):
                                                       'surface_fwhm',
                                                       'filter_type',
                                                       'timepoints_to_remove',
-                                                      'do_whitening']),
+                                                      'do_whitening',
+                                                      'regress_before_PCA']),
                         name='inputspec')
 
     # Separate input node for FWHM
@@ -316,6 +317,8 @@ def create_prep(name='preproc'):
                     getmask, 'inputspec.source_file')
     preproc.connect(inputnode, 'num_noise_components',
                     compcor, 'inputspec.num_components')
+    preproc.connect(inputnode, 'regress_before_PCA',
+                    compcor, 'inputspec.regress_before_PCA')
     preproc.connect(motion_correct, 'out_file',
                     compcor, 'inputspec.realigned_file')
     preproc.connect(meanfunc, 'outputspec.mean_image',

bips/workflows/workflow1.py

@@ -234,6 +234,8 @@ def prep_workflow(c, fieldmap):
     preproc.inputs.inputspec.ad_zthresh = c.z_thresh
     preproc.inputs.inputspec.tr = c.TR
     preproc.inputs.inputspec.do_slicetime = c.do_slicetiming
+    preproc.inputs.inputspec.regress_before_PCA = c.regress_before_PCA
+
     if c.do_slicetiming:
         preproc.inputs.inputspec.sliceorder = c.SliceOrder
     else:
@@ -368,6 +370,7 @@ def create_view():
                       label='Artifact Detection',show_border=True),
                 Group(Item(name='compcor_select'),
                       Item(name='num_noise_components'),
+                      Item(name='regress_before_PCA'),
                       label='CompCor',show_border=True),
                 Group(Item(name="smooth_type"),
                       Item(name='fwhm', editor=CSVListEditor()),

bips/workflows/workflow2.py

@@ -109,6 +109,7 @@ def prep_workflow(c, fieldmap):
     preproc.inputs.inputspec.smooth_type = c.smooth_type
     preproc.inputs.inputspec.surface_fwhm = c.surface_fwhm
     preproc.inputs.inputspec.num_noise_components = c.num_noise_components
+    preproc.inputs.inputspec.regress_before_PCA = c.regress_before_PCA
     preproc.crash_dir = c.crash_dir
     modelflow.connect(infosource, 'subject_id', preproc, 'inputspec.fssubject_id')
     preproc.inputs.inputspec.fssubject_dir = c.surf_dir
@@ -253,6 +254,7 @@ def create_view():
                       label='Artifact Detection',show_border=True),
                 Group(Item(name='compcor_select'),
                       Item(name='num_noise_components'),
+                      Item(name='regress_before_PCA'),
                       label='CompCor',show_border=True),
                 Group(Item(name='reg_params'),
                       label='Nuisance Filtering',show_border=True),