Merge pull request #387 from tsalo/mbme-reproin

ENH: Support SBRef and phase data in ReproIn heuristic

Author: yarikoptic

heudiconv/convert.py

@@ -518,6 +518,8 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
         bids_files = (sorted(res.outputs.bids)
                       if len(res.outputs.bids) == len(res_files)
                       else [None] * len(res_files))
+        # preload since will be used in multiple spots
+        bids_metas = [load_json(b) for b in bids_files if b]
 
         ###   Do we have a multi-echo series?   ###
         #   Some Siemens sequences (e.g. CMRR's MB-EPI) set the label 'TE1',
@@ -531,19 +533,17 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
 
         # Check for varying echo times
         echo_times = sorted(list(set(
-            load_json(b).get('EchoTime', nan)
-            for b in bids_files
+            b.get('EchoTime', nan)
+            for b in bids_metas
             if b
         )))
 
         is_multiecho = len(echo_times) > 1
 
         ### Loop through the bids_files, set the output name and save files
-        for fl, suffix, bids_file in zip(res_files, suffixes, bids_files):
+        for fl, suffix, bids_file, bids_meta in zip(res_files, suffixes, bids_files, bids_metas):
 
             # TODO: monitor conversion duration
-            if bids_file:
-                fileinfo = load_json(bids_file)
 
             # set the prefix basename for this specific file (we'll modify it,
             # and we don't want to modify it for all the bids_files):
@@ -552,11 +552,18 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
             # _sbref sequences reconstructing magnitude and phase generate
             # two NIfTI files IN THE SAME SERIES, so we cannot just add
             # the suffix, if we want to be bids compliant:
-            if bids_file and this_prefix_basename.endswith('_sbref'):
+            if bids_meta and this_prefix_basename.endswith('_sbref') \
+                    and len(suffixes) > len(echo_times):
+                if len(suffixes) != len(echo_times)*2:
+                    lgr.warning(
+                        "Got %d suffixes for %d echo times, which isn't "
+                        "multiple of two as if it was magnitude + phase pairs",
+                        len(suffixes), len(echo_times)
+                    )
                 # Check to see if it is magnitude or phase reconstruction:
-                if 'M' in fileinfo.get('ImageType'):
+                if 'M' in bids_meta.get('ImageType'):
                     mag_or_phase = 'magnitude'
-                elif 'P' in fileinfo.get('ImageType'):
+                elif 'P' in bids_meta.get('ImageType'):
                     mag_or_phase = 'phase'
                 else:
                     mag_or_phase = suffix
@@ -585,12 +592,12 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
             # (Note: it can be _sbref and multiecho, so don't use "elif"):
             # For multi-echo sequences, we have to specify the echo number in
             # the file name:
-            if bids_file and is_multiecho:
+            if bids_meta and is_multiecho:
                 # Get the EchoNumber from json file info.  If not present, use EchoTime
-                if 'EchoNumber' in fileinfo.keys():
-                    echo_number = fileinfo['EchoNumber']
+                if 'EchoNumber' in bids_meta:
+                    echo_number = bids_meta['EchoNumber']
                 else:
-                    echo_number = echo_times.index(fileinfo['EchoTime']) + 1
+                    echo_number = echo_times.index(bids_meta['EchoTime']) + 1
 
                 supported_multiecho = ['_bold', '_phase', '_epi', '_sbref', '_T1w', '_PDT2']
                 # Now, decide where to insert it.

heudiconv/external/dlad.py

@@ -10,7 +10,7 @@
 
 lgr = logging.getLogger(__name__)
 
-MIN_VERSION = '0.12.2'
+MIN_VERSION = '0.12.4'
 
 
 def prepare_datalad(studydir, outdir, sid, session, seqinfo, dicoms, bids):
@@ -177,4 +177,4 @@ def mark_sensitive(ds, path_glob):
         init=dict([('distribution-restrictions', 'sensitive')]),
         recursive=True)
     if inspect.isgenerator(res):
-        res = list(res)
+        res = list(res)

heudiconv/heuristics/reproin.py

@@ -514,10 +514,10 @@ def infotodict(seqinfo):
             # 3 - Image IOD specific specialization (optional)
             dcm_image_iod_spec = s.image_type[2]
             image_type_seqtype = {
-                'P': 'fmap',   # phase
+                # Note: P and M are too generic to make a decision here, could be
+                #  for different seqtypes (bold, fmap, etc)
                 'FMRI': 'func',
                 'MPR': 'anat',
-                # 'M': 'func',  "magnitude"  -- can be for scout, anat, bold, fmap
                 'DIFFUSION': 'dwi',
                 'MIP_SAG': 'anat',  # angiography
                 'MIP_COR': 'anat',  # angiography
@@ -570,29 +570,55 @@ def infotodict(seqinfo):
         #     prefix = ''
         prefix = ''
 
+        #
+        # Figure out the seqtype_label (BIDS _suffix)
+        #
+        # If none was provided -- let's deduce it from the information we find:
         # analyze s.protocol_name (series_id is based on it) for full name mapping etc
-        if seqtype == 'func' and not seqtype_label:
-            if '_pace_' in series_spec:
-                seqtype_label = 'pace'  # or should it be part of seq-
-            else:
-                # assume bold by default
-                seqtype_label = 'bold'
-
-        if seqtype == 'fmap' and not seqtype_label:
-            if not dcm_image_iod_spec:
-                raise ValueError("Do not know image data type yet to make decision")
-            seqtype_label = {
-                # might want explicit {file_index}  ?
-                # _epi for pepolar fieldmaps, see
-                # https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-4-multiple-phase-encoded-directions-pepolar
-                'M': 'epi' if 'dir' in series_info else 'magnitude',
-                'P': 'phasediff',
-                'DIFFUSION': 'epi',  # according to KODI those DWI are the EPIs we need
-            }[dcm_image_iod_spec]
-
-        # label for dwi as well
-        if seqtype == 'dwi' and not seqtype_label:
-            seqtype_label = 'dwi'
+        if not seqtype_label:
+            if seqtype == 'func':
+                if '_pace_' in series_spec:
+                    seqtype_label = 'pace'  # or should it be part of seq-
+                elif 'P' in s.image_type:
+                    seqtype_label = 'phase'
+                elif 'M' in s.image_type:
+                    seqtype_label = 'bold'
+                else:
+                    # assume bold by default
+                    seqtype_label = 'bold'
+            elif seqtype == 'fmap':
+                # TODO: support phase1 phase2 like in "Case 2: Two phase images ..."
+                if not dcm_image_iod_spec:
+                    raise ValueError("Do not know image data type yet to make decision")
+                seqtype_label = {
+                    # might want explicit {file_index}  ?
+                    # _epi for pepolar fieldmaps, see
+                    # https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#case-4-multiple-phase-encoded-directions-pepolar
+                    'M': 'epi' if 'dir' in series_info else 'magnitude',
+                    'P': 'phasediff',
+                    'DIFFUSION': 'epi',  # according to KODI those DWI are the EPIs we need
+                }[dcm_image_iod_spec]
+            elif seqtype == 'dwi':
+                # label for dwi as well
+                seqtype_label = 'dwi'
+
+        #
+        # Even if seqtype_label was provided, for some data we might need to override,
+        # since they are complementary files produced along-side with original
+        # ones.
+        #
+        if s.series_description.endswith('_SBRef'):
+            seqtype_label = 'sbref'
+
+        if not seqtype_label:
+            # Might be provided by the bids ending within series_spec, we would
+            # just want to check if that the last element is not _key-value pair
+            bids_ending = series_info.get('bids', None)
+            if not bids_ending \
+                    or "-" in bids_ending.split('_')[-1]:
+                lgr.warning(
+                    "We ended up with an empty label/suffix for %r",
+                    series_spec)
 
         run = series_info.get('run')
         if run is not None:

heudiconv/info.py

@@ -42,7 +42,7 @@
 EXTRA_REQUIRES = {
     'tests': TESTS_REQUIRES,
     'extras': [],  # Requires patched version ATM ['dcmstack'],
-    'datalad': ['datalad >=0.12.2']
+    'datalad': ['datalad >=0.12.3']
 }
 
 # Flatten the lists