RF: Update anatomical derivatives for RC1

Author: effigies

.circleci/ds054_outputs.txt

@@ -6,15 +6,15 @@ fmriprep/logs/CITATION.md
 fmriprep/logs/CITATION.tex
 fmriprep/sub-100185
 fmriprep/sub-100185/anat
-fmriprep/sub-100185/anat/sub-100185_class-CSF_probseg.nii.gz
-fmriprep/sub-100185/anat/sub-100185_class-GM_probseg.nii.gz
-fmriprep/sub-100185/anat/sub-100185_class-WM_probseg.nii.gz
 fmriprep/sub-100185/anat/sub-100185_desc-brain_mask.nii.gz
 fmriprep/sub-100185/anat/sub-100185_desc-preproc_T1w.nii.gz
 fmriprep/sub-100185/anat/sub-100185_dseg.nii.gz
 fmriprep/sub-100185/anat/sub-100185_from-MNI152NLin2009cAsym_to-T1w_xfm.h5
 fmriprep/sub-100185/anat/sub-100185_from-orig_to-T1w_xfm.txt
 fmriprep/sub-100185/anat/sub-100185_from-T1w_target-MNI152NLin2009cAsym_xfm.h5
+fmriprep/sub-100185/anat/sub-100185_label-CSF_probseg.nii.gz
+fmriprep/sub-100185/anat/sub-100185_label-GM_probseg.nii.gz
+fmriprep/sub-100185/anat/sub-100185_label-WM_probseg.nii.gz
 fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_class-CSF_probseg.nii.gz
 fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_class-GM_probseg.nii.gz
 fmriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_class-WM_probseg.nii.gz

fmriprep/interfaces/bids.py

@@ -163,6 +163,8 @@ class DerivativesDataSinkInputSpec(BaseInterfaceInputSpec):
     in_file = InputMultiPath(File(exists=True), mandatory=True,
                              desc='the object to be saved')
     source_file = File(exists=False, mandatory=True, desc='the input func file')
+    space = traits.Str(desc='Label for space field')
+    desc = traits.Str(desc='Label for description field')
     keep_dtype = traits.Bool(False, usedefault=True, desc='keep datatype suffix')
     suffix = traits.Str('', mandatory=True, desc='suffix appended to source_file')
     extra_values = traits.List(traits.Str)
@@ -244,14 +246,19 @@ def _run_interface(self, runtime):
 
         base_fname = op.join(out_path, src_fname)
 
-        formatstr = '{bname}_{suffix}{dtype}{ext}'
+        formatstr = '{bname}_{space}{desc}{suffix}{dtype}{ext}'
         if len(self.inputs.in_file) > 1 and not isdefined(self.inputs.extra_values):
-            formatstr = '{bname}_{suffix}{i:04d}{dtype}{ext}'
+            formatstr = '{bname}_{space}{desc}{suffix}{i:04d}{dtype}{ext}'
+
+        space = 'space-{space}'.format(self.inputs.space) if self.inputs.space else ''
+        desc = 'desc-{desc}'.format(self.inputs.desc) if self.inputs.desc else ''
 
         self._results['compression'] = []
         for i, fname in enumerate(self.inputs.in_file):
             out_file = formatstr.format(
                 bname=base_fname,
+                space=space,
+                desc=desc,
                 suffix=self.inputs.suffix,
                 i=i,
                 dtype='' if not self.inputs.keep_dtype else ('_%s' % dtype),

fmriprep/workflows/anatomical.py

@@ -1227,70 +1227,68 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
     t1_name = pe.Node(niu.Function(function=fix_multi_T1w_source_name), name='t1_name')
 
     ds_t1_preproc = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix='preproc'),
+        DerivativesDataSink(base_directory=output_dir, desc='preproc', keep_dtype=True),
         name='ds_t1_preproc', run_without_submitting=True)
 
     ds_t1_mask = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix='brainmask'),
+        DerivativesDataSink(base_directory=output_dir, desc='brain', suffix='mask'),
         name='ds_t1_mask', run_without_submitting=True)
 
     ds_t1_seg = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix='dtissue'),
+        DerivativesDataSink(base_directory=output_dir, suffix='dseg'),
         name='ds_t1_seg', run_without_submitting=True)
 
     ds_t1_tpms = pe.Node(
         DerivativesDataSink(base_directory=output_dir,
-                            suffix='class-{extra_value}_probtissue'),
+                            suffix='label-{extra_value}_probseg'),
         name='ds_t1_tpms', run_without_submitting=True)
     ds_t1_tpms.inputs.extra_values = ['CSF', 'GM', 'WM']
 
-    suffix_fmt = 'space-{}_{}'.format
     ds_t1_mni = pe.Node(
         DerivativesDataSink(base_directory=output_dir,
-                            suffix=suffix_fmt(template, 'preproc')),
+                            space=template, desc='preproc', keep_dtype=True),
         name='ds_t1_mni', run_without_submitting=True)
 
     ds_mni_mask = pe.Node(
         DerivativesDataSink(base_directory=output_dir,
-                            suffix=suffix_fmt(template, 'brainmask')),
+                            space=template, desc='brain', suffix='mask'),
         name='ds_mni_mask', run_without_submitting=True)
 
     ds_mni_seg = pe.Node(
         DerivativesDataSink(base_directory=output_dir,
-                            suffix=suffix_fmt(template, 'dtissue')),
+                            space=template, suffix='dseg'),
         name='ds_mni_seg', run_without_submitting=True)
 
     ds_mni_tpms = pe.Node(
         DerivativesDataSink(base_directory=output_dir,
-                            suffix=suffix_fmt(template, 'class-{extra_value}_probtissue')),
+                            space=template, suffix='label-{extra_value}_probseg'),
         name='ds_mni_tpms', run_without_submitting=True)
     ds_mni_tpms.inputs.extra_values = ['CSF', 'GM', 'WM']
 
     # Transforms
-    suffix_fmt = 'space-{}_target-{}_{}'.format
+    suffix_fmt = 'from-{}_to-{}_mode-image_xfm'.format
     ds_t1_mni_inv_warp = pe.Node(
         DerivativesDataSink(base_directory=output_dir,
-                            suffix=suffix_fmt(template, 'T1w', 'warp')),
+                            suffix=suffix_fmt(template, 'T1w')),
         name='ds_t1_mni_inv_warp', run_without_submitting=True)
 
     ds_t1_template_transforms = pe.MapNode(
-        DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('orig', 'T1w', 'affine')),
+        DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('orig', 'T1w')),
         iterfield=['source_file', 'in_file'],
         name='ds_t1_template_transforms', run_without_submitting=True)
 
-    suffix_fmt = 'target-{}_{}'.format
     ds_t1_mni_warp = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt(template, 'warp')),
+        DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('T1w', template)),
         name='ds_t1_mni_warp', run_without_submitting=True)
 
     lta_2_itk = pe.Node(LTAConvert(out_itk=True), name='lta_2_itk')
 
     ds_t1_fsnative = pe.Node(
-        DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('fsnative', 'affine')),
+        DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('T1w', 'fsnative')),
         name='ds_t1_fsnative', run_without_submitting=True)
 
     name_surfs = pe.MapNode(GiftiNameSource(pattern=r'(?P<LR>[lr])h.(?P<surf>.+)_converted.gii',
-                                            template='{surf}.{LR}.surf'),
+                                            template='hemi-{LR}_{surf}.surf'),
                             iterfield='in_file',
                             name='name_surfs',
                             run_without_submitting=True)