Make sure only dwi images get *.bvec and *.bval files

`dcm2niix` produces *.bvec/*.bval files whenever it extracts an image collected with a DW sequence. However, BIDS only accepts those files in the `dwi` folders.

Author: pvelasco

heudiconv/convert.py

@@ -674,9 +674,14 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
         return
 
     if isdefined(res.outputs.bvecs) and isdefined(res.outputs.bvals):
-        outname_bvecs, outname_bvals = prefix + '.bvec', prefix + '.bval'
-        safe_movefile(res.outputs.bvecs, outname_bvecs, overwrite)
-        safe_movefile(res.outputs.bvals, outname_bvals, overwrite)
+        if prefix_dirname.endswith('dwi'):
+            outname_bvecs, outname_bvals = prefix + '.bvec', prefix + '.bval'
+            safe_movefile(res.outputs.bvecs, outname_bvecs, overwrite)
+            safe_movefile(res.outputs.bvals, outname_bvals, overwrite)
+        else:
+            os.remove(res.outputs.bvecs)
+            os.remove(res.outputs.bvals)
+            lgr.debug("%s and %s were removmed", res.outputs.bvecs, res.outputs.bvals)
 
     if isinstance(res_files, list):
         res_files = sorted(res_files)

heudiconv/heuristics/test_b0dwi_for_fmap.py

@@ -0,0 +1,33 @@
+"""Heuristic to extract a b-value=0 DWI image (basically, a SE-EPI)
+both as a fmap and as dwi
+
+It is used just to test that a 'DIFFUSION' image that the user
+chooses to extract as fmap (pepolar case) doesn't produce _bvecs/
+_bvals json files, while it does for dwi images
+"""
+
+
+def create_key(template, outtype=('nii.gz',), annotation_classes=None):
+    if template is None or not template:
+        raise ValueError('Template must be a valid format string')
+    return template, outtype, annotation_classes
+
+def infotodict(seqinfo):
+    """Heuristic evaluator for determining which runs belong where
+
+    allowed template fields - follow python string module:
+
+    item: index within category
+    subject: participant id
+    seqitem: run number during scanning
+    subindex: sub index within group
+    """
+    fmap = create_key('sub-{subject}/fmap/sub-{subject}_acq-b0dwi_epi')
+    dwi = create_key('sub-{subject}/dwi/sub-{subject}_acq-b0dwi_dwi')
+
+    info = {fmap: [], dwi: []}
+    for s in seqinfo:
+        if 'DIFFUSION' in s.image_type and 'FieldMap' in s.series_description:
+            info[fmap].append(s.series_id)
+            info[dwi].append(s.series_id)
+    return info

heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00001.dcm

@@ -1,11 +1,16 @@
 """Test functions in heudiconv.convert module.
 """
+import os.path as op
+from glob import glob
+
 import pytest
+from .utils import TESTS_DATA_PATH
 
 from heudiconv.convert import (update_complex_name,
                                update_multiecho_name,
                                update_uncombined_name)
 from heudiconv.bids import BIDSError
+from heudiconv.cli.run import main as runner
 
 
 def test_update_complex_name():
@@ -76,3 +81,29 @@ def test_update_uncombined_name():
     out_fn_true = 'sub-X_ses-Y_task-Z_run-01_ch-04_bold'
     out_fn_test = update_uncombined_name(metadata, fn, channel_names)
     assert out_fn_test == out_fn_true
+
+
+def test_b0dwi_for_fmap(tmpdir):
+    """Make sure that we don't copy .bvec and .bval files
+    when the modality is not dwi.
+    We check it by extracting a b-value=0 dwi image as fmap and dwi
+    """
+    tmppath = tmpdir.strpath
+    subID = 'b0dwiForFmap'
+    args = (
+        "-c dcm2niix -o %s -b -f test_b0dwi_for_fmap --files %s -s %s"
+        % (tmpdir, op.join(TESTS_DATA_PATH, 'b0dwiForFmap'), subID)
+    ).split(' ')
+    runner(args)
+
+    # check that the fmap directory has been extracted and it doesn't contain
+    # any *.bvec or *.bval files
+    assert op.isdir(op.join(tmppath, 'sub-%s', 'fmap') % (subID))
+    for ext in ['bval', 'bvec']:
+        assert not glob(op.join(tmppath, 'sub-%s', 'fmap', 'sub-%s_*.%s') % (subID, subID, ext))
+
+    # check that the dwi directory has been extracted and it does contain a
+    # *.bvec and a *.bval files
+    assert op.isdir(op.join(tmppath, 'sub-%s', 'dwi') % (subID))
+    for ext in ['bval', 'bvec']:
+        assert glob(op.join(tmppath, 'sub-%s', 'dwi', 'sub-%s_*.%s') % (subID, subID, ext))