yarikoptic
commented
6 months ago as you have discovered later, it is a duplicate of
- https://github.com/nipy/heudiconv/issues/670 thus closing this one
Closed s-madhavan closed 6 months ago
yarikoptic
commented
6 months ago as you have discovered later, it is a duplicate of
Summary
Hi everyone. I am doing Dicom to Nifti conversion through singularity using a heudiconv.sif file. I keep running into this error and don't think it is an issue with my dicom files because I've been able to individually convert some of them to nifti but when I run it all together I get the following error
Error: numpy.exceptions.AxisError: axis 1 is out of bounds for array of dimension 1
I've never had this issue before. Has anyone else run into this? If yes, how do I resolve this issue using singularity. This is my current command to do Dicom to Nifti:
subject=$1 session=$2 echo "Starting BIDS conversion for subject" $subject $session
singularity run --cleanenv \ /fs/ess/PAS2302/Subbi/TURBO/TERBO/heudiconv_latest.sif \ -d /fs/ess/PAS2302/Subbi/TURBO/TERBO/data//DICOM/{subject}/SCANS/DICOM/ \ -o /fs/ess/PAS2302/Subbi/TURBO/TERBO/Nifti \ -f /fs/ess/PAS2302/Subbi/TURBO/TERBO/Scripts/TERBO/YT/convert_TERBO_Miami_SM_YT.py \ -s $subject \ -ss $session \ -c dcm2niix \ -b \ --overwrite ;
echo "Finished subject" $subject $session
Platform details:
Choose one:
[ ] Local environment
[x] Container
Heudiconv version: