External Email - Use Caution Hi Bruce,
Thanks for getting back to me. I wanted to write a bash script that would allow me run recon-all, I'm just not sure how to set it up. Is it possible to use a .txt file to do this? I know others have used a .txt file containing the subject IDs to find the correct files. e.g. Create a txt file with all the subject names (as they appear on their respective folders). Name that txt file whatever you want (like "* subs.txt*") and save it somewhere in one of the paths (we use /Users/* Home_User*). Then in terminal, after setting the environments for Freesurfer and the subjects directory, insert the following: for SubjectName in `cat *subs.txt*` do recon-all -s $SubjectName -all -qcache done Would this work if all my subjects are in separate sub directories? I apologise if I'm not explaining myself clearly, but I'm a complete novice. Kind regards, Benjamin ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: 27 June 2019 15:38 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all multiple subjects 'for' loop? Hi Benjamin you can run them all in the same terminal by backgrounding them (adding the & character at the end of the command line) cheers Bruce On Thu, 27 Jun 2019, Benjamin Stott wrote: > > External Email - Use Caution > > Hello, > I would like to run recon-all on multiple subjects. I have 650 subjects, so > running them in separate > terminals isn't an option. Each subject has their own folder (e.g. > sub-CC121428) containing a single > T1w.nii.gz file. > > Unfortunately, I have very little experience coding. I appreciate any advice > you can offer. > > Benjamin > > >
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