Description
Hi,
When I'm trying to use heudiconv with the '-p' flag, I get the following error (it works properly without using this flag):
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'session': 'baseline', 'outdir': '/SPINE_BIDS_Test_server-side/nifti/', 'subject': '004'}
INFO: Processing 480 dicoms
INFO: Analyzing 480 dicoms
INFO: Generated sequence info with 3 entries
INFO: Doing conversion using dcm2niix
INFO: Converting /SPINE_BIDS_Test_server-side/nifti/sub-004/ses-baseline/anat/sub-004_ses-baseline_FLAIR (128 DICOMs) -> /SPINE_BIDS_Test_server-side/nifti/sub-004/ses-baseline/anat . Converter: dcm2niix . Output types: ('nii.gz',)
INFO: Executing node convert in dir: /tmp/heudiconvdcm23WAK6/convert
INFO: Running: dcm2niix -b y -z i -x n -t n -m n -f anat -o /tmp/heudiconvdcm23WAK6/convert -s n -v n /tmp/heudiconvdcm23WAK6/convert/1.3.12.2.1107.5.2.7.20107.4.0.1576580820461847.dcm
Traceback (most recent call last):
File "/usr/local/bin/heudiconv", line 2197, in
main()
File "/usr/local/bin/heudiconv", line 2189, in main
return _main(args)
File "/usr/local/bin/heudiconv", line 2052, in _main
min_meta=args.minmeta)
File "/usr/local/bin/heudiconv", line 1407, in convert_dicoms
min_meta=min_meta)
File "/usr/local/bin/heudiconv", line 911, in convert
res = convertnode.run()
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 372, in run
self._run_interface()
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 482, in _run_interface
self._result = self._run_command(execute)
File "/opt/conda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 613, in _run_command
result = self._interface.run()
File "/opt/conda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1130, in run
prov_record = write_provenance(results)
File "/opt/conda/lib/python2.7/site-packages/nipype/utils/provenance.py", line 289, in write_provenance
ps.add_results(results)
File "/opt/conda/lib/python2.7/site-packages/nipype/utils/provenance.py", line 416, in add_results
for key, value in list(get_info().items()):
File "/opt/conda/lib/python2.7/site-packages/nipype/init.py", line 47, in get_info
return _get_pkg_info(os.path.dirname(file))
File "/opt/conda/lib/python2.7/site-packages/nipype/pkg_info.py", line 88, in get_pkg_info
src, hsh = pkg_commit_hash(pkg_path)
File "/opt/conda/lib/python2.7/site-packages/nipype/pkg_info.py", line 56, in pkg_commit_hash
archive_subst = cfg_parser.get('commit hash', 'archive_subst_hash')
File "/opt/conda/lib/python2.7/site-packages/backports/configparser/init.py", line 811, in get
d)
File "/opt/conda/lib/python2.7/site-packages/backports/configparser/init.py", line 384, in before_get
self._interpolate_some(parser, option, L, value, section, defaults, 1)
File "/opt/conda/lib/python2.7/site-packages/backports/configparser/init.py", line 434, in _interpolate_some
"found: %r" % (rest,))
backports.configparser.InterpolationSyntaxError: '%' must be followed by '%' or '(', found: u'%h'
My script :
#!/bin/bash
wrk_dir='/home/gregory/Documents/SPINE_BIDS_Test_server-side/'
nifti_dir='/nifti/'
nifti_pat='/SPINE_BIDS_Test_server-side/'$nifti_dir
dicom_dir='/SPINE_BIDS_Test_server-side/DICOM-lite/DICOM_sub-{subject}/ses-{session}/*/*.dcm'
heuristic_file='/SPINE_BIDS_Test_server-side/heuristic.py'
cd $wrk_dir
sudo docker run --rm -it -v $PWD:/SPINE_BIDS_Test_server-side nipy/heudiconv \
-d ${dicom_dir} \
-s "004" \
-ss "baseline" \
-f ${heuristic_file} \
-b \
-p \
--minmeta \
-c dcm2niix \
-o ${nifti_pat}