Merge pull request #43 from AlanKuurstra/akdev

update cfmm_bruker heuristic, switch to forked heudiconv

Dockerfile

@@ -5,7 +5,7 @@ LABEL maintainer="<[email protected]>"
 ENV DCM2NIIXTAG v1.0.20230411
 
 #heudiconv version:
-ENV HEUDICONVTAG v0.13.1
+ENV HEUDICONVTAG unstacked_dcm
 
 #bids validator version:
 ENV BIDSTAG 1.9.7
@@ -37,9 +37,22 @@ RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
         python3=3.9.2-3 \
         python3-pip=20.3.4-4+deb11u1 \
-    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
-    && pip install --no-cache-dir heudiconv==${HEUDICONVTAG}
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+        git \
+        python3-setuptools \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && git clone https://github.com/AlanKuurstra/heudiconv.git /src/heudiconv \
+    && git -C /src/heudiconv checkout ${HEUDICONVTAG}
+WORKDIR /src/heudiconv
+RUN python3 -m pip install --no-cache-dir -r /src/heudiconv/requirements.txt \
+    && python3 -m pip install --no-cache-dir versioningit \
+    && python3 /src/heudiconv/setup.py install
+
+# install pybruker for cfmm_bruker heuristic
+RUN python3 -m pip install --no-cache-dir pybruker --index-url https://gitlab.com/api/v4/projects/29466867/packages/pypi/simple
 
 # install BIDS Validator
 RUN apt-get update -qq \

heuristics/cfmm_bruker.py

@@ -1,10 +1,17 @@
-import os
+from heudiconv.utils import set_readonly, save_json
+import json
+import logging
+from pybruker.jcamp import jcamp_read
+import pydicom
 
-def create_key(template, outtype=('nii.gz'), annotation_classes=None):
+lgr = logging.getLogger("heudiconv")
+
+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
 
@@ -27,11 +34,9 @@ def infotodict(seqinfo):
     FLASH_MT_OFF = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MToff_run-{item:02d}_FLASH')
     dwi = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_run-{item:02d}_dwi')
 
-    MP2RAGE_T1map = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MP2RAGE_run-{item:02d}_T1map')
     MP2RAGE_invs = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-Inversions_run-{item:02d}_MP2RAGE')
     MP2RAGE_UNI = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-UNI_run-{item:02d}_T1w')
 
-    MP2RAGE_T1map_l = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-LoResMP2RAGE_run-{item:02d}_T1map')
     MP2RAGE_invs_l = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-LoResInversions_run-{item:02d}_MP2RAGE')
     MP2RAGE_UNI_l = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-LoResUNI_run-{item:02d}_T1w')
 
@@ -42,7 +47,10 @@ def infotodict(seqinfo):
 
     T2_TurboRARE = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-TurboRARE_run-{item:02d}_T2w')
 
-    info = { FLASH_T1:[],FLASH_MT_ON:[],FLASH_MT_OFF:[],dwi:[],MP2RAGE_T1map:[],MP2RAGE_invs:[],MP2RAGE_UNI:[],MP2RAGE_T1map_l:[],MP2RAGE_invs_l:[],MP2RAGE_UNI_l:[],MEGRE_mag:[],MEGRE_complex:[],T2_TurboRARE:[]}
+    # where does bids_subject_session_prefix come from? or item? heudiconv special variables? can we get the task type (visual/audio) somehow?
+    BLOCK_EPI =  create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-unknown_acq-BlockEPI_run-{item:02d}_bold')
+
+    info = { FLASH_T1:[],FLASH_MT_ON:[],FLASH_MT_OFF:[],dwi:[],MP2RAGE_invs:[],MP2RAGE_UNI:[],MP2RAGE_invs_l:[],MP2RAGE_UNI_l:[],MEGRE_mag:[],MEGRE_complex:[],T2_TurboRARE:[],BLOCK_EPI:[]}
 
     for idx, s in enumerate(seqinfo):
 
@@ -56,23 +64,19 @@ def infotodict(seqinfo):
             else:
                 info[FLASH_MT_ON].append({'item': s.series_id})
 
-        elif ('DTI' in s.protocol_name):
+        elif ('dti' in s.protocol_name.lower()):
             info[dwi].append({'item': s.series_id})
 
-        elif ('MP2RAGE' in s.series_description.strip()):
+        elif ('cfmmMP2RAGE' in s.series_description.strip()):
           if (s.dim1 > 64):
             if  ('0001' in s.dcm_dir_name.strip()):
-                info[MP2RAGE_T1map].append({'item': s.series_id})
-            elif  ('0002' in s.dcm_dir_name.strip()):
                 info[MP2RAGE_invs].append({'item': s.series_id})
-            else:
+            elif  ('0002' in s.dcm_dir_name.strip()):
                 info[MP2RAGE_UNI].append({'item': s.series_id})
           else:
             if  ('0001' in s.dcm_dir_name.strip()):
-                info[MP2RAGE_T1map_l].append({'item': s.series_id})
-            elif  ('0002' in s.dcm_dir_name.strip()):
                 info[MP2RAGE_invs_l].append({'item': s.series_id})
-            else:
+            elif  ('0002' in s.dcm_dir_name.strip()):
                 info[MP2RAGE_UNI_l].append({'item': s.series_id})
 
         elif ('T2star' in s.series_description.strip()):
@@ -82,7 +86,21 @@ def infotodict(seqinfo):
                 info[MEGRE_mag].append({'item': s.series_id})
         elif ( 'T2_TurboRARE' in s.series_description.strip()):
             info[T2_TurboRARE].append({'item': s.series_id})
-
-
+        elif ( 'blockEPI' in s.series_description.strip()):
+            info[BLOCK_EPI].append({'item': s.series_id})
 
     return info
+
+def custom_callable(outfile, outtype, infiles):
+    dcm_filename = infiles[0]
+    bruker_parameters_jcamp = pydicom.read_file(dcm_filename, stop_before_pixels=True).get((0x0177, 0x1100))
+    if bruker_parameters_jcamp:
+        jcamp_dict = jcamp_read(bruker_parameters_jcamp.value)
+        scaninfo_filename = outfile + '.json'
+        lgr.info(f"Adding bruker parameters to {scaninfo_filename}")
+        with open(scaninfo_filename, 'r') as f:
+            info_dict = json.load(f)
+        info_dict['cfmm_bruker_parameters'] = jcamp_dict
+        # if blockEPI then use bruker parameters to create events.tsv
+        save_json(scaninfo_filename, info_dict)
+        set_readonly(scaninfo_filename)