ENH: Allows the user to save the Phoenix Report (Siemens) in the sourcedata

This way the user can go back to the scanner and import the exact same protocol that was run for a given subject, improving reproducibility.

Author: pvelasco

heudiconv/dicoms.py

@@ -265,8 +265,13 @@ def group_dicoms_into_seqinfos(files, grouping, file_filter=None,
         series_id = '-'.join(map(str, series_id))
         if mw.image_shape is None:
             # this whole thing has no image data (maybe just PSg DICOMs)
-            # nothing to see here, just move on
-            continue
+            # If this is a Siemens PhoenixZipReport or PhysioLog, keep it:
+            if mw.dcm_data.SeriesDescription == 'PhoenixZIPReport':
+                # give it a dummy shape, so that we can continue:
+                mw.image_shape = (0, 0, 0)
+            else:
+                # nothing to see here, just move on
+                continue
         seqinfo = create_seqinfo(mw, series_files, series_id)
 
         if per_studyUID:

heudiconv/heuristics/bids_PhoenixReport.py

@@ -0,0 +1,38 @@
+"""Heuristic demonstrating conversion of the PhoenixZIPReport from Siemens.
+
+It only cares about converting a series with have PhoenixZIPReport in their
+series_description and outputs **only to sourcedata**.
+"""
+
+
+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
+    """
+    sbref = create_key('sub-{subject}/func/sub-{subject}_task-QA_sbref', outtype=('nii.gz', 'dicom',))
+    scout = create_key('sub-{subject}/anat/sub-{subject}_T1w', outtype=('nii.gz', 'dicom',))
+    phoenix_doc = create_key('sub-{subject}/misc/sub-{subject}_phoenix', outtype=('dicom',))
+
+    info = {sbref: [], scout: [], phoenix_doc: []}
+    for s in seqinfo:
+        if (
+            'PhoenixZIPReport' in s.series_description
+            and s.image_type[3] == 'CSA REPORT'
+        ):
+            info[phoenix_doc].append({'item': s.series_id})
+        if 'scout' in s.series_description.lower():
+            info[scout].append({'item': s.series_id})
+
+    return info

heudiconv/tests/data/Phoenix/01+AA/01+AA+00001.dcm

@@ -1,12 +1,18 @@
 import os.path as op
 import json
+from glob import glob
 
 import pytest
 
 from heudiconv.external.pydicom import dcm
 from heudiconv.cli.run import main as runner
 from heudiconv.convert import nipype_convert
-from heudiconv.dicoms import parse_private_csa_header, embed_dicom_and_nifti_metadata
+from heudiconv.dicoms import (
+    parse_private_csa_header,
+    embed_dicom_and_nifti_metadata,
+    group_dicoms_into_seqinfos,
+    OrderedDict,
+)
 from .utils import (
     assert_cwd_unchanged,
     TESTS_DATA_PATH,
@@ -64,3 +70,18 @@ def test_embed_dicom_and_nifti_metadata(tmpdir):
 
     assert out3.pop("existing") == "data"
     assert out3 == out2
+
+
+def test_group_dicoms_into_seqinfos(tmpdir):
+    """Tests for group_dicoms_into_seqinfos"""
+
+    # 1) Check that it works for PhoenixDocuments:
+    # set up testing files
+    dcmfolder = op.join(TESTS_DATA_PATH, 'Phoenix')
+    dcmfiles = glob(op.join(dcmfolder, '*', '*.dcm'))
+
+    seqinfo = group_dicoms_into_seqinfos(dcmfiles, 'studyUID', flatten=True)
+
+    assert type(seqinfo) is OrderedDict
+    assert len(seqinfo) == len(dcmfiles)
+    assert [s.series_description for s in seqinfo] == ['AAHead_Scout_32ch-head-coil', 'PhoenixZIPReport']

heudiconv/tests/data/Phoenix/99+PhoenixDocument/99+PhoenixDocument+00001.dcm

@@ -176,3 +176,20 @@ def test_notop(tmpdir, bidsoptions):
             assert not op.exists(pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4', fname))
         else:
             assert op.exists(pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4', fname))
+
+
+def test_phoenix_doc_conversion(tmpdir):
+    tmppath = tmpdir.strpath
+    subID = 'Phoenix'
+    args = (
+        "-c dcm2niix -o %s -b -f bids_PhoenixReport --files %s -s %s"
+        % (tmpdir, pjoin(TESTS_DATA_PATH, 'Phoenix'), subID)
+    ).split(' ')
+    runner(args)
+
+    # check that the Phoenix document has been extracted (as gzipped dicom) in
+    # the sourcedata/misc folder:
+    assert op.exists(pjoin(tmppath, 'sourcedata', 'sub-%s', 'misc', 'sub-%s_phoenix.dicom.tgz') % (subID, subID))
+    # check that no "sub-<subID>/misc" folder has been created in the BIDS
+    # structure:
+    assert not op.exists(pjoin(tmppath, 'sub-%s', 'misc') % subID)