Error while using '--with-prov' flag

[gregblt]

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_Testserver-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}

[satra]

@gregorymichelet - we will be addressing this with the latest nipype release in a couple of weeks. just bear with us till then.

[mgxd]

This should be fixed since nipy/nipype#2701