External Email - Use Caution
i there,
I am attempting to perform the recon-all in parallel command.
When I run this command I get the following message:
ls: *.nii: No such file or directory
The following command is:
bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/tbi/TBN bash-3.2$ echo $SUBJECTS_DIR /Applications/freesurfer/7.2.0/tbi/TBN bash-3.2$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache ls: *.nii: No such file or directory Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite:
Tange, O. (2022, August 22). GNU Parallel 20220822 ('Rushdie'). Zenodo. https://secure-web.cisco.com/1mGw517t0yBXkztNqf01JZCPURoO6_GwJZcmOf9XN0Bit3s...
This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
More about funding GNU Parallel and the citation notice: https://secure-web.cisco.com/1qeJBgbE0rR_XWDJGaS_dtrryFt6t984jQGxAubuxxJ-dkU...
To silence this citation notice: run 'parallel --citation' once.
I have also attached a screenshot of the file with the nii files to help.
I am seeking some support to overcome this issue.
Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Platform: OSX 7.2.0
Thank you in advance!
Kind regards, Ellie
