Merge pull request #738 from swederik/bf/parcellate

BF: Fixing path issues for CMTK Parcellate dilated ROI files

Author: chrisgorgo

nipype/interfaces/cmtk/parcellation.py

@@ -258,7 +258,7 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
             rois[idx] = int(brv['dn_correspondence_id'])
 
         # store volume eg in ROI_scale33.nii.gz
-        out_roi = op.join(output_dir, 'ROI_%s.nii.gz' % parcellation_name)
+        out_roi = op.abspath('ROI_%s.nii.gz' % parcellation_name)
 
         # update the header
         hdr = aseg.get_header()
@@ -290,7 +290,7 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation):
                 rois[xx[j], yy[j], zz[j]] = value
 
         # store volume eg in ROIv_scale33.nii.gz
-        out_roi = op.join(output_dir, 'ROIv_%s.nii.gz' % parcellation_name)
+        out_roi = op.abspath('ROIv_%s.nii.gz' % parcellation_name)
         iflogger.info("Save output image to %s" % out_roi)
         img = nb.Nifti1Image(rois, aseg.get_affine(), hdr2)
         nb.save(img, out_roi)
@@ -303,7 +303,6 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
     fs_dir = op.join(subjects_dir, subject_id)
     cmp_config = cmp.configuration.PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
-    log = cmp_config.get_logger()
     pgpath = cmp_config._get_lausanne_parcellation(
         'Lausanne2008')[parcellation_name]['node_information_graphml']
     # load ribbon as basis for white matter mask
@@ -422,8 +421,6 @@ def create_wm_mask(subject_id, subjects_dir, fs_dir, parcellation_name):
     wmmask[idx] = 1
 
     # check if we should subtract the cortical rois from this parcellation
-    parval = cmp_config._get_lausanne_parcellation(
-        'Lausanne2008')[parcellation_name]
     iflogger.info("Loading %s to subtract cortical ROIs from white matter mask" % ('ROI_%s.nii.gz' % parcellation_name))
     roi = nb.load(op.join(op.curdir, 'ROI_%s.nii.gz' % parcellation_name))
     roid = roi.get_data()
@@ -448,28 +445,25 @@ def crop_and_move_datasets(subject_id, subjects_dir, fs_dir, parcellation_name,
     cmp_config = cmp.configuration.PipelineConfiguration()
     cmp_config.parcellation_scheme = "Lausanne2008"
     log = cmp_config.get_logger()
-    pgpath = cmp_config._get_lausanne_parcellation(
-        'Lausanne2008')[parcellation_name]['node_information_graphml']
-    reg_path = out_roi_file
     output_dir = op.abspath(op.curdir)
 
     iflogger.info("Cropping and moving datasets to %s" % output_dir)
     ds = [
-        (op.join(fs_dir, 'mri', 'aseg.nii.gz'), op.join(
-         output_dir, 'aseg.nii.gz')),
-        (op.join(fs_dir, 'mri', 'ribbon.nii.gz'), op.join(
-         output_dir, 'ribbon.nii.gz')),
-        (op.join(fs_dir, 'mri', 'fsmask_1mm.nii.gz'), op.join(
-         output_dir, 'fsmask_1mm.nii.gz')),
+        (op.join(fs_dir, 'mri', 'aseg.nii.gz'),
+         op.abspath('aseg.nii.gz')),
+        (op.join(fs_dir, 'mri', 'ribbon.nii.gz'),
+         op.abspath('ribbon.nii.gz')),
+        (op.join(fs_dir, 'mri', 'fsmask_1mm.nii.gz'),
+         op.abspath('fsmask_1mm.nii.gz')),
         (op.join(fs_dir, 'label', 'cc_unknown.nii.gz'),
-         op.join(output_dir, 'cc_unknown.nii.gz'))
+         op.abspath('cc_unknown.nii.gz'))
     ]
 
-    ds.append((op.join(op.curdir, 'ROI_%s.nii.gz' % parcellation_name),
-              op.join(op.curdir, 'ROI_HR_th.nii.gz')))
+    ds.append((op.abspath('ROI_%s.nii.gz' % parcellation_name),
+              op.abspath('ROI_HR_th.nii.gz')))
     if(dilation==True):
-    	ds.append((op.join(op.curdir, 'ROIv_%s.nii.gz' %
-              parcellation_name), op.join(op.curdir, 'ROIv_HR_th.nii.gz')))
+    	ds.append((op.abspath('ROIv_%s.nii.gz' % parcellation_name),
+            op.abspath('ROIv_HR_th.nii.gz')))
     orig = op.join(fs_dir, 'mri', 'orig', '001.mgz')
     for d in ds:
         iflogger.info("Processing %s:" % d[0])