That is an issue with ls, which is not a freesurfer problem, eg, if you run ls *.nii you will get the same error it seems to think that there are no nii files in that folder

On 9/9/2022 6:04 AM, Ellie Shaw wrote:

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. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://doi.org/10.5281/zenodo.7015730 https://secure-web.cisco.com/1mGw517t0yBXkztNqf01JZCPURoO6_GwJZcmOf9XN0Bit3sTTg0ceeN1EKQLZG4eIYgkSTUAQLwmqh-h82MN7vkpzO6wKeuWyYxvEL1DptqCZDAMkMwLKJUYVFOxVS4GVPMjuwpsvvDRG4trH3qAQ6taD3WwIaPInoCK_aL5eW9bpPRphnbuylmz6h5ZLnqZgAXyhZeyPxT5Bmhtb3WGzG0v7dRUuObTPT-jHdrOt0NRarHoBw3UMBBTLJipGJMvJSo97amDzg7-Bg4fElP-5hZB9ihjn1BCU_TaojD9SIaTlTOx_6-1-vcm5oFTd2RZr2W35745p53DjP4RxPWg2Mg/https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.7015730

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: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.gnu.org/software/parallel/parallel_design.html#citation-notice https://secure-web.cisco.com/1qeJBgbE0rR_XWDJGaS_dtrryFt6t984jQGxAubuxxJ-dkUJLO3WH4_789BhYN7ztyHE8w4S5a-DCk5OyLKiKy4TzjT4yRv5KMcdrEcsN-1AyL_QF7asNjm_-wuKXChiQOapMT9GvUFkd6B8RvuvRMuVQEpzfOz7P9cg8uwp45ovxzRUdTddUusfXlAXT1nfQdPFtCbDcDihUpxi1rvRSIqAT_RIpVZHh9iBSx4BuK2t4gLhNK_5NBxIJJPXDgwMpYd_LVU4PYcsaSIfL01WdNpu72Lw_JfILM675DCEjhDUft2vkFQKtkehBybTCiYI34YMPtL8Mzl7maiZmRFmYfA/https%3A%2F%2Fwww.gnu.org%2Fsoftware%2Fparallel%2Fparallel_design.html%23citation-notice

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

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