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sotnir / NENAH-BIDS

A collaborate platform for streamlining a BIDS workflow for the NENAH study, on the linux workstation based at University of Southampton.
https://www.southampton.ac.uk/cndng
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Working for NENAH046 #115

Closed yukaizou2015 closed 8 months ago

yukaizou2015 commented 2 years ago

MRIQC anat sub-NENAH046_run-1_T1w 0.5 sub-NENAH046_run-2_T1w 0.5 sub-NENAH046_run-2_T1w :+1:

MRIQC func No fMRI data in /rawdata

yukaizou2015 commented 2 years ago

From derivatives/preprocessing_logs/sub-NENAH046/sub-NENAH046_DcmSourcedata_to_NiftiRawdata.log:

Traceback (most recent call last):
  File "/opt/miniconda-latest/bin/heudiconv", line 33, in <module>
    sys.exit(load_entry_point('heudiconv', 'console_scripts', 'heudiconv')())
  File "/src/heudiconv/heudiconv/cli/run.py", line 24, in main
    workflow(**kwargs)
  File "/src/heudiconv/heudiconv/main.py", line 351, in workflow
    grouping=grouping,)
  File "/src/heudiconv/heudiconv/convert.py", line 216, in prep_conversion
    dcmconfig=dcmconfig,)
  File "/src/heudiconv/heudiconv/convert.py", line 481, in convert
    overwrite=overwrite)
  File "/src/heudiconv/heudiconv/convert.py", line 678, in save_converted_files
    safe_movefile(res.outputs.bvecs, outname_bvecs, overwrite)
  File "/src/heudiconv/heudiconv/utils.py", line 363, in safe_movefile
    return _safe_op_file(src, dest, "move", overwrite=overwrite)
  File "/src/heudiconv/heudiconv/utils.py", line 375, in _safe_op_file
    if op.realpath(src) == op.realpath(dest):
  File "/opt/miniconda-latest/lib/python3.6/posixpath.py", line 394, in realpath
    filename = os.fspath(filename)
TypeError: expected str, bytes or os.PathLike object, not TraitListObject

Split into NENAH046_ses1_syngo1, NENAH046_ses1_syngo2, NENAH046_ses2 in /sourcedata.

/sourcedata /rawdata contains /fmap and /func?
NENAH046_ses1_syngo1 no
NENAH046_ses1_syngo2 yes
NENAH046_ses2 yes

Reorganised into /rawdata/sub-NENAH046_newFunc/func:

total 311496
-r--rw-r-- 1 yz23e20 neuropediatrics     2146 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-1_bold.json
-r--rw-r-- 1 yz23e20 neuropediatrics 40929796 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-1_bold.nii.gz
-rw-rw-r-- 1 yz23e20 neuropediatrics      116 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-1_events.tsv
-r--rw-r-- 1 yz23e20 neuropediatrics     2146 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-2_bold.json
-r--rw-r-- 1 yz23e20 neuropediatrics 78180558 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-2_bold.nii.gz
-rw-rw-r-- 1 yz23e20 neuropediatrics      116 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-2_events.tsv
-r--rw-r-- 1 yz23e20 neuropediatrics     2147 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-3_bold.json
-r--rw-r-- 1 yz23e20 neuropediatrics 71212233 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-3_bold.nii.gz
-rw-rw-r-- 1 yz23e20 neuropediatrics      116 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-3_events.tsv
-r--rw-r-- 1 yz23e20 neuropediatrics     2139 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-4_bold.json
-r--rw-r-- 1 yz23e20 neuropediatrics 57683909 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-4_bold.nii.gz
-rw-rw-r-- 1 yz23e20 neuropediatrics      116 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-4_events.tsv
-r--rw-r-- 1 yz23e20 neuropediatrics     2144 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-5_bold.json
-r--rw-r-- 1 yz23e20 neuropediatrics 70914790 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-5_bold.nii.gz
-rw-rw-r-- 1 yz23e20 neuropediatrics      116 Mar 24 14:40 sub-NENAH046_task-rest_dir-AP_run-5_events.tsv