Hi Padma,
It looks like tcsh isn't installed. Can you try installing it by running
``` sudo apt update sudo apt install tcsh ```
-Paul ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of priya padma priya@phenomx.ai Sent: Wednesday, October 12, 2022 3:16 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Running recon-all in parallel
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Hello team,
As freesurfer takes lot of time for processing one subject, I was searching on how to run recon-all for multiple subjects in parallel and I found the following in Andy's brain book doc
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS...https://secure-web.cisco.com/1MEMXaE4I_nNiI-Rew0Vd8aEQB5KqBzrJ54sB6YQjjf_p8mYy6QKljeDcXuzbfx_nGEh14jSussDu49EGjDdEtDy9i7nDhGycEoHv-C2WdqjEmvt-sDEUJM-T9VjrR0zRNIhfY7ECdqIaqaG2WkqiywZzfdJZhHpjGK9swf1GFUb_-eEozUbvipLWVN8IAFcqY4aWeE3uWj5lMUxf0M1XqbbZ9TyAVLjHStOCwXvzLFIPWu48DBHirGnhI9VbENX2WHXdoy9URKf61mD3lkWRUTZbWfSLFh29HXyQGOxfD4F6Rg6lRhPNX1ZVN4110JWOGtMVqTIrqq2zR3MHV-vbYw/https%3A%2F%2Fandysbrainbook.readthedocs.io%2Fen%2Flatest%2FFreeSurfer%2FFS_ShortCourse%2FFS_04_ReconAllParallel.html
and ran
$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache
and I get the error "/usr/bin/bash: /home/***/***/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory "
I believe that this is not the right command for linux, ubuntu 20 OS but I am not sure.
Could anyone help me with this?
Thank you
-- Best Regards Padma Priya AI Developer [https://secure-web.cisco.com/1XLVnI0aLlqbfbCotrXgyfGAqS76ynzDA16AK0UPYPBFVyM...] PhenoMx, Inc. priya@phenomx.aimailto:priya@phenomx.ai | (+82)10-5405-2685