Merge pull request #1321 from oesteban/fix/1000

[ENH] Template-based masking of EPI boldrefs
nipreps · Oct 25, 2018 · 874c4ce · 874c4ce
2 parents a0460f9 + 7535a08
commit 874c4ce
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Showing 17 changed files with 230 additions and 56 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -742,14 +742,22 @@ workflows:
       - get_regression_data:
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore:
+                - /docs?\/.*/
+                - /ds005\/.*/
+                - /ds054\/.*/
+                - /ds210\/.*/
 
       - build_docs:
           requires:
             - build
           filters:
             branches:
-              ignore: /tests?\/.*/
+              ignore:
+                - /tests?\/.*/
+                - /ds005\/.*/
+                - /ds054\/.*/
+                - /ds210\/.*/
             tags:
               only: /.*/
 
@@ -770,7 +778,11 @@ workflows:
             - get_regression_data
           filters:
             branches:
-              ignore: /docs?\/.*/
+              ignore: 
+                - /docs?\/.*/
+                - /ds005\/.*/
+                - /ds054\/.*/
+                - /ds210\/.*/
             tags:
               only: /.*/
 
@@ -783,6 +795,8 @@ workflows:
               ignore:
                 - /docs?\/.*/
                 - /tests?\/.*/
+                - /ds054\/.*/
+                - /ds210\/.*/
             tags:
               only: /.*/
 
@@ -795,6 +809,8 @@ workflows:
               ignore:
                 - /docs?\/.*/
                 - /tests?\/.*/
+                - /ds005\/.*/
+                - /ds210\/.*/
             tags:
               only: /.*/
 
@@ -808,6 +824,8 @@ workflows:
               ignore:
                 - /docs?\/.*/
                 - /tests?\/.*/
+                - /ds005\/.*/
+                - /ds054\/.*/
             tags:
               only: /.*/
 

diff --git a/.circleci/ds005_outputs.txt b/.circleci/ds005_outputs.txt
@@ -36,8 +36,8 @@ fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.dtseries.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.dtseries.nii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
@@ -52,8 +52,8 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-T1w_label-aseg_ds
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_regressors.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.dtseries.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.dtseries.nii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz

diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_partial_outputs.txt
@@ -36,8 +36,8 @@ fmriprep/sub-01/func
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_AROMAnoiseICs.csv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_regressors.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-MELODIC_mixing.tsv
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.dtseries.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.dtseries.nii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-L.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-fsaverage5_hemi-R.func.gii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz

diff --git a/docker/scripts/get_templates.sh b/docker/scripts/get_templates.sh
@@ -2,14 +2,18 @@
 
 MNI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705eb594d9001ed622649"
 MNI_SHA256="608b1d609255424d51300e189feacd5ec74b04e244628303e802a6c0b0f9d9db"
-ASYM_09C_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9"
-ASYM_09C_SHA256="a24699ba0d13f72d0f8934cc211cb80bfd9c9a077b481d9b64295cf5275235a9"
+ASYM_09C_TEMPLATE_OLD="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9"
+ASYM_09C_SHA256_OLD="a24699ba0d13f72d0f8934cc211cb80bfd9c9a077b481d9b64295cf5275235a9"
+ASYM_09C_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b0dbce20f461a000db8fa3d"
+ASYM_09C_SHA256="2851302474359c2c48995155aadb48b861e5dcf87aefda71af8010f671e8ed66"
 OASIS_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/584123a29ad5a1020913609d"
 OASIS_SHA256="d87300e91346c16f55baf6f54f5f990bc020b61e8d5df9bcc3abb0cc4b943113"
-NKI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/59cd90f46c613b02b3d79782"
-NKI_SHA256="4bba067f6675d15be96b205cb227e18a540673fd7e4577e13feedcef3a6f0ec5"
+NKI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5bc3fad82aa873001bc5a553"
+NKI_SHA256="9c08713d067bcf13baa61b01a9495e526b55d1f148d951da01e082679f076fa9"
 OASIS_DKT31_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b16f17aeca4a80012bd7542"
 OASIS_DKT31_SHA256="623fa7141712b1a7263331dba16eb069a4443e9640f52556c89d461611478145"
+EPI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5bc12155ac011000176bff82"
+EPI_SHA256="fcd6980ef98c9d7622c6dc2a7747ff51ba3909d98e2a740df9a8265d50920d1b"
 
 GET(){
     URL=$1; SHA256=$2;
@@ -28,6 +32,8 @@ GET(){
 set -e
 echo "Getting MNI template"
 GET "$MNI_TEMPLATE" "$MNI_SHA256"
+echo "Getting (deprecated version of) MNI152NLin2009cAsym template"
+GET "$ASYM_09C_TEMPLATE_OLD" "$ASYM_09C_SHA256_OLD"
 echo "Getting MNI152NLin2009cAsym template"
 GET "$ASYM_09C_TEMPLATE" "$ASYM_09C_SHA256"
 echo "Getting OASIS template"
@@ -36,4 +42,6 @@ echo "Getting NKI template"
 GET "$NKI_TEMPLATE" "$NKI_SHA256"
 echo "Getting OASIS DKT31 template"
 GET "$OASIS_DKT31_TEMPLATE" "$OASIS_DKT31_SHA256"
+echo "Getting fMRIPrep's BOLDref template"
+GET "$EPI_TEMPLATE" "$EPI_SHA256"
 echo "Done!"
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -29,4 +29,4 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.4.2
+    - niworkflows==0.4.4
diff --git a/fmriprep/__about__.py b/fmriprep/__about__.py
@@ -98,7 +98,7 @@
     'pybids==0.6.5',
     'nitime',
     'nipype>=1.1.3',
-    'niworkflows>=0.4.4',
+    'niworkflows==0.4.4',
     'statsmodels',
     'seaborn',
     'indexed_gzip>=0.8.2',

diff --git a/fmriprep/data/epi_atlasbased_brainmask.json b/fmriprep/data/epi_atlasbased_brainmask.json
@@ -0,0 +1,20 @@
+{
+    "winsorize_upper_quantile": 0.98,
+    "winsorize_lower_quantile": 0.05,
+    "float": true,
+    "metric": ["Mattes"],
+    "metric_weight": [1],
+    "radius_or_number_of_bins": [64],
+    "transforms": ["Affine"],
+    "transform_parameters": [[0.1]],
+    "number_of_iterations": [[200]],
+    "convergence_window_size": [10],
+    "convergence_threshold": [1e-09],
+    "sampling_strategy": ["Random", "Random"],
+    "smoothing_sigmas": [[2]],
+    "sigma_units": ["mm", "mm", "mm"],
+    "shrink_factors": [[2]],
+    "sampling_percentage": [0.2],
+    "use_histogram_matching": [true],
+    "use_estimate_learning_rate_once": [true]
+}
diff --git a/fmriprep/interfaces/__init__.py b/fmriprep/interfaces/__init__.py
@@ -5,7 +5,7 @@
     ReadSidecarJSON, DerivativesDataSink, BIDSDataGrabber, BIDSFreeSurferDir, BIDSInfo
 )
 from .images import (
-    IntraModalMerge, ValidateImage, TemplateDimensions, Conform
+    IntraModalMerge, ValidateImage, TemplateDimensions, Conform, MatchHeader
 )
 from .freesurfer import (
     StructuralReference, MakeMidthickness, FSInjectBrainExtracted,

diff --git a/fmriprep/interfaces/images.py b/fmriprep/interfaces/images.py
@@ -479,6 +479,53 @@ def _run_interface(self, runtime):
         return runtime
 
 
+class MatchHeaderInputSpec(BaseInterfaceInputSpec):
+    reference = File(exists=True, mandatory=True,
+                     desc='NIfTI file with reference header')
+    in_file = File(exists=True, mandatory=True,
+                   desc='NIfTI file which header will be checked')
+
+
+class MatchHeaderOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='NIfTI file with fixed header')
+
+
+class MatchHeader(SimpleInterface):
+    input_spec = MatchHeaderInputSpec
+    output_spec = MatchHeaderOutputSpec
+
+    def _run_interface(self, runtime):
+        refhdr = nb.load(self.inputs.reference).header.copy()
+        imgnii = nb.load(self.inputs.in_file)
+        imghdr = imgnii.header.copy()
+
+        imghdr['dim_info'] = refhdr['dim_info']  # dim_info is lost sometimes
+
+        # Set qform
+        qform = refhdr.get_qform()
+        qcode = int(refhdr['qform_code'])
+        if not np.allclose(qform, imghdr.get_qform()):
+            LOGGER.warning(
+                'q-forms of reference and mask are substantially different')
+        imghdr.set_qform(qform, qcode)
+
+        # Set sform
+        sform = refhdr.get_sform()
+        scode = int(refhdr['sform_code'])
+        if not np.allclose(sform, imghdr.get_sform()):
+            LOGGER.warning(
+                's-forms of reference and mask are substantially different')
+        imghdr.set_sform(sform, scode)
+
+        out_file = fname_presuffix(self.inputs.in_file, suffix='_hdr',
+                                   newpath=runtime.cwd)
+
+        imgnii.__class__(imgnii.get_data(), imghdr.get_best_affine(),
+                         imghdr).to_filename(out_file)
+        self._results['out_file'] = out_file
+        return runtime
+
+
 def reorient(in_file, newpath=None):
     """Reorient Nifti files to RAS"""
     out_file = fname_presuffix(in_file, suffix='_ras', newpath=newpath)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -394,9 +394,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         ]),
     ])
 
-    # The first reference uses T2 contrast enhancement
-    bold_reference_wf = init_bold_reference_wf(
-        omp_nthreads=omp_nthreads, enhance_t2=True)
+    # Generate a tentative boldref
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
 
     # Top-level BOLD splitter
     bold_split = pe.Node(FSLSplit(dimension='t'), name='bold_split',
@@ -924,7 +923,7 @@ def init_func_derivatives_wf(output_dir, output_spaces, template, freesurfer,
                 CiftiNameSource(), iterfield=['variant'], name='name_cifti',
                 mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
             cifti_bolds = pe.MapNode(
-                DerivativesDataSink(base_directory=output_dir, desc='preproc', compress=False),
+                DerivativesDataSink(base_directory=output_dir, compress=False),
                 iterfield=['in_file', 'suffix'], name='cifti_bolds',
                 run_without_submitting=True, mem_gb=DEFAULT_MEMORY_MIN_GB)
             cifti_key = pe.MapNode(DerivativesDataSink(

diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
@@ -324,7 +324,7 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
     merge = pe.Node(Merge(compress=use_compression), name='merge', mem_gb=mem_gb)
 
     # Generate a reference on the target T1w space
-    gen_final_ref = init_bold_reference_wf(omp_nthreads)
+    gen_final_ref = init_bold_reference_wf(omp_nthreads, pre_mask=True)
 
     workflow.connect([
         (inputnode, merge_xforms, [('itk_bold_to_t1', 'in1')]),
@@ -334,6 +334,7 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, use_fieldwarp=False,
         (gen_ref, bold_to_t1w_transform, [('out_file', 'reference_image')]),
         (bold_to_t1w_transform, merge, [('out_files', 'in_files')]),
         (merge, gen_final_ref, [('out_file', 'inputnode.bold_file')]),
+        (mask_t1w_tfm, gen_final_ref, [('output_image', 'inputnode.bold_mask')]),
         (merge, outputnode, [('out_file', 'bold_t1')]),
         (gen_final_ref, outputnode, [('outputnode.ref_image', 'bold_t1_ref')]),
     ])

diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
@@ -301,7 +301,8 @@ def _aslist(in_value):
                     mem_gb=mem_gb * 3)
 
     # Generate a reference on the target T1w space
-    gen_final_ref = init_bold_reference_wf(omp_nthreads)
+    gen_final_ref = init_bold_reference_wf(
+        omp_nthreads=omp_nthreads, pre_mask=True)
 
     workflow.connect([
         (inputnode, merge_xforms, [('t1_2_mni_forward_transform', 'in1'),
@@ -311,6 +312,7 @@ def _aslist(in_value):
         (inputnode, bold_to_mni_transform, [('bold_split', 'input_image')]),
         (bold_to_mni_transform, merge, [('out_files', 'in_files')]),
         (merge, gen_final_ref, [('out_file', 'inputnode.bold_file')]),
+        (mask_mni_tfm, gen_final_ref, [('output_image', 'inputnode.bold_mask')]),
         (merge, outputnode, [('out_file', 'bold_mni')]),
         (gen_final_ref, outputnode, [('outputnode.ref_image', 'bold_mni_ref')]),
     ])

diff --git a/fmriprep/workflows/bold/tests/test_util.py b/fmriprep/workflows/bold/tests/test_util.py
@@ -58,7 +58,7 @@ def symmetric_overlap(img1, img2):
     )
 ])
 def test_masking(input_fname, expected_fname):
-    bold_reference_wf = init_bold_reference_wf(omp_nthreads=1, enhance_t2=True)
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=1)
     bold_reference_wf.inputs.inputnode.bold_file = input_fname
 
     # Reconstruct base_fname from above