ENH: generate CIFTI derivatives

.circleci/config.yml

@@ -82,8 +82,8 @@ jobs:
     steps:
       - restore_cache:
           keys:
-            - data-v4-{{ epoch }}
-            - data-v4-
+            - data-v5-{{ epoch }}
+            - data-v5-
       - run:
           name: Get test data from ds000005
           command: |
@@ -151,7 +151,7 @@ jobs:
             - ds054/nipype.cfg
             - ds000210/nipype.cfg
       - save_cache:
-         key: data-v4-{{ epoch }}
+         key: data-v5-{{ epoch }}
          paths:
             - /tmp/data
             - /tmp/ds005/derivatives/freesurfer
@@ -331,7 +331,7 @@ jobs:
                 --ignore-aroma-denoising-errors --mem_mb 4096 \
                 --output-space T1w template fsaverage5 \
                 --template-resampling-grid native \
-                --nthreads 2 -vv
+                --nthreads 2 --cifti-output -vv
       - run:
           name: Move intermediate results for second run
           command: |
@@ -357,7 +357,7 @@ jobs:
                 --ignore-aroma-denoising-errors --mem_mb 4096 \
                 --output-space T1w template fsaverage5 \
                 --template-resampling-grid native \
-                --nthreads 2 -vv
+                --nthreads 2 --cifti-output -vv
       - run:
           name: Checking outputs of partial fMRIPrep run
           command: |
@@ -553,7 +553,7 @@ jobs:
                 /tmp/data/ds000210 /tmp/ds000210/derivatives participant \
                 --fs-no-reconall --t2s-coreg --use-syn-sdc \
                 --template-resampling-grid native \
-                --debug --write-graph --mem_mb 4096 --nthreads 2 -vv 
+                --debug --write-graph --mem_mb 4096 --nthreads 2 -vv
       - run:
           name: Checking outputs of fMRIPrep
           command: |

.circleci/ds005_outputs.txt

@@ -44,6 +44,8 @@ fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
@@ -56,6 +58,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-T1w_preproc.
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_confounds.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_MELODICmix.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-cifti_variant-space1_preproc.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-fsaverage5.R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz

.circleci/ds005_partial_outputs.txt

@@ -44,6 +44,8 @@ fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_confounds.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_MELODICmix.tsv
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-cifti_variant-space1_preproc.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-fsaverage5.R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz

docs/environment.yml

@@ -28,4 +28,4 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.3.7 
+    - niworkflows>=0.3.7

docs/outputs.rst

@@ -8,14 +8,14 @@ Outputs of FMRIPREP
 
 FMRIPREP generates three broad classes of outcomes:
 
-  1. **Visual QA (quality assessment) reports**: 
+  1. **Visual QA (quality assessment) reports**:
      one :abbr:`HTML (hypertext markup language)` per subject,
      that allows the user a thorough visual assessment of the quality
      of processing and ensures the transparency of fMRIPrep operation.
 
   2. **Pre-processed imaging data** which are derivatives of the original
      anatomical and functional images after various preparation procedures
-     have been applied. For example, 
+     have been applied. For example,
      :abbr:`INU (intensity non-uniformity)`-corrected versions of the T1-weighted
      image (per subject), the brain mask, or :abbr:`BOLD (blood-oxygen level dependent)`
      images after head-motion correction, slice-timing correction and aligned into
@@ -41,7 +41,7 @@ Each report is self contained and thus can be easily shared with collaborators (
 Preprocessed data (fMRIPrep *derivatives*)
 ------------------------------------------
 
-There are additional files, called "Derivatives", written to 
+There are additional files, called "Derivatives", written to
 ``<output dir>/fmriprep/sub-<subject_label>/``. See the
 `BIDS Derivatives <https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/edit?usp=sharing>`_
 spec for more information.
@@ -87,6 +87,11 @@ Surface output spaces include ``fsnative`` (full density subject-specific mesh),
 
 - (optional) ``*bold_space-<space>.[LR].func.gii`` Motion-corrected EPI file sampled to surface ``<space>``
 
+EPIs can be saved as a CIFTI dtseries file.
+
+- (optional) ``*bold_space-cifti_variant-<variant>_preproc.dtseries.nii`` Motion-corrected EPI converted to CIFTI filetype. Sub-cortical representations
+  are volumetric (supported spaces: ``MNI152NLin2009cAsym``), while cortical representations are sampled to surface (supported spaces: ``fsaverage5``, ``fsaverage6``)
+
 
 .. _fsderivs:
 
@@ -144,7 +149,7 @@ These are :abbr:`TSV (tab-separated values)` tables, which look like the example
   -1.41   0.29    0.96    13.06   0.99    0.01    -0.04   0.07    0.10    0.31    0.47    0.27    -0.22   0.09    0.11    0.12    0.56    0.14    0.00    0.00    0.00    0.07    0.00    0.00    0.00    -0.67   0.44    0.25    -0.57
 
 
-Each row of the file corresponds to one time point found in the 
+Each row of the file corresponds to one time point found in the
 corresponding :abbr:`BOLD (blood-oxygen level dependent)` time-series
 (stored in ``<output_folder>/fmriprep/sub-<sub_id>/func/sub-<sub_id>_task-<task_id>_run-<run_id>_bold_preproc.nii.gz``).
 
@@ -154,13 +159,13 @@ the :abbr:`CSF (cerebro-spinal fluid)` and :abbr:`WM (white matter)` mask across
 derivative of RMS variance over voxels (or :abbr:`DVARS (D referring to difference, )`) that can be
 standardized (``stdDVARS``), non-standardized (``non-stdDVARS``), and voxel-wise standardized (``vx-wisestdDVARS``);
 the ``FrameDisplacement`` is a quantification of the estimated bulk-head motion; ``X``, ``Y``, ``Z``, ``RotX``,
-``RotY``, ``RotZ`` are the actual 6 rigid-body transform parameters estimated by FMRIPREP; 
+``RotY``, ``RotZ`` are the actual 6 rigid-body transform parameters estimated by FMRIPREP;
 the ``NonSteadyStateOutlier00`` column is ``1`` when a non-steady state was found (typically at the beginning of
-the scan) and ``0`` elsewhere; and finally six noise components ``aCompCorXX`` calculated using 
-:abbr:`CompCor (Component Based Noise Correction Method)` 
-and five noise components ``AROMAaggrCompXX`` if 
+the scan) and ``0`` elsewhere; and finally six noise components ``aCompCorXX`` calculated using
+:abbr:`CompCor (Component Based Noise Correction Method)`
+and five noise components ``AROMAaggrCompXX`` if
 :abbr:`ICA (independent components analysis)`-:abbr:`AROMA (Automatic Removal Of Motion Artifacts)` was enabled.
 
-All these confounds can be used to perform *scrubbing* and *censoring* of outliers, 
+All these confounds can be used to perform *scrubbing* and *censoring* of outliers,
 in the subsequent first-level analysis when building the design matrix,
 and in group level analysis.

docs/workflows.rst

@@ -34,6 +34,7 @@ is presented below:
                                 output_spaces=['T1w', 'fsnative',
                                               'template', 'fsaverage5'],
                                 medial_surface_nan=False,
+                                cifti_output=False,
                                 ignore=[],
                                 debug=False,
                                 low_mem=False,
@@ -232,6 +233,7 @@ BOLD preprocessing
                               output_spaces=['T1w', 'fsnative',
                                              'template', 'fsaverage5'],
                               medial_surface_nan=False,
+                              cifti_output=False,
                               debug=False,
                               low_mem=False,
                               use_bbr=True,

fmriprep/cli/run.py

@@ -175,18 +175,24 @@ def get_parser():
 
     # FreeSurfer options
     g_fs = parser.add_argument_group('Specific options for FreeSurfer preprocessing')
-    g_fs.add_argument('--fs-no-reconall', '--no-freesurfer',
-                      action='store_false', dest='run_reconall',
-                      help='disable FreeSurfer surface preprocessing.'
-                      ' Note : `--no-freesurfer` is deprecated and will be removed in 1.2.'
-                      ' Use `--fs-no-reconall` instead.')
-    g_fs.add_argument('--no-submm-recon', action='store_false', dest='hires',
-                      help='disable sub-millimeter (hires) reconstruction')
     g_fs.add_argument(
         '--fs-license-file', metavar='PATH', type=os.path.abspath,
         help='Path to FreeSurfer license key file. Get it (for free) by registering'
              ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
 
+    # Surface generation xor
+    g_surfs = parser.add_argument_group('Surface preprocessing options')
+    g_surfs.add_argument('--no-submm-recon', action='store_false', dest='hires',
+                         help='disable sub-millimeter (hires) reconstruction')
+    g_surfs_xor = g_surfs.add_mutually_exclusive_group()
+    g_surfs_xor.add_argument('--cifti-output', action='store_true', default=False,
+                             help='output BOLD files as CIFTI dtseries')
+    g_surfs_xor.add_argument('--fs-no-reconall', '--no-freesurfer',
+                             action='store_false', dest='run_reconall',
+                             help='disable FreeSurfer surface preprocessing.'
+                             ' Note : `--no-freesurfer` is deprecated and will be removed in 1.2.'
+                             ' Use `--fs-no-reconall` instead.')
+
     g_other = parser.add_argument_group('Other options')
     g_other.add_argument('-w', '--work-dir', action='store',
                          help='path where intermediate results should be stored')
@@ -449,6 +455,7 @@ def build_workflow(opts, retval):
         output_spaces=opts.output_space,
         template=opts.template,
         medial_surface_nan=opts.medial_surface_nan,
+        cifti_output=opts.cifti_output,
         template_out_grid=template_out_grid,
         hires=opts.hires,
         use_bbr=opts.use_bbr,

fmriprep/interfaces/bids.py

@@ -163,6 +163,8 @@ class DerivativesDataSinkInputSpec(BaseInterfaceInputSpec):
     source_file = File(exists=False, mandatory=True, desc='the input func file')
     suffix = traits.Str('', mandatory=True, desc='suffix appended to source_file')
     extra_values = traits.List(traits.Str)
+    compress = traits.Bool(desc="force compression (True) or uncompression (False)"
+                                " of the output file (default: same as input)")
 
 
 class DerivativesDataSinkOutputSpec(TraitedSpec):
@@ -202,9 +204,10 @@ def __init__(self, out_path_base=None, **inputs):
     def _run_interface(self, runtime):
         src_fname, _ = _splitext(self.inputs.source_file)
         _, ext = _splitext(self.inputs.in_file[0])
-        compress = ext == '.nii'
-        if compress:
-            ext = '.nii.gz'
+        if self.inputs.compress is True and not ext.endswith('.gz'):
+            ext += '.gz'
+        elif self.inputs.compress is False and ext.endswith('.gz'):
+            ext = ext[:-3]
 
         m = BIDS_NAME.search(src_fname)
 
@@ -246,7 +249,7 @@ def _run_interface(self, runtime):
             if isdefined(self.inputs.extra_values):
                 out_file = out_file.format(extra_value=self.inputs.extra_values[i])
             self._results['out_file'].append(out_file)
-            if compress:
+            if ext.endswith('.gz'):
                 with open(fname, 'rb') as f_in:
                     with gzip.open(out_file, 'wb') as f_out:
                         copyfileobj(f_in, f_out)