Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data

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Hi Falk,

Thank you for your response. I see, that makes sense. I'll use one of those options to make sure my processed data goes into the correct folder from now on.

One more follow up question - I located my processed data in the default directory and used mv to move it to my fs-subjects folder. My question is: Do these processed data folders for a given subject, eg "sub101-sesFU" function independently, or does the fact that some of them were exported to the default directory rather than my designated fs-subjects folder mean that it will affect any group-level analyzing? I ask this because I know there is an "fsaverage" directory (whose purpose I do not really understand) in both the default directory and in my fs-subjects directory. I am unsure if exporting processed data to different directories affects anything and that I would have to rerun a subject, or if everything is good to move forward.

Thank you very much for your help!

All my best, Joanna

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.de Sent: Thursday, May 12, 2022 2:27 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data

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Hi Joanna,

once you close the terminal window, you have to export the variable SUBJECTS_DIR again. Your processed data is potentially in the default directory and you can access it by typing "cd $SUBJECTS_DIR" (without quotations marks) into the terminal. There is two ways (and probably a lot more) around that:

1. You can add the -sd flag to recon-all which will change it temporarily, e.g. recon-all -all -i <input data> -s >subject ID> -sd /home/developer/FreeSurfer/fs-subjects 2. You can add a line to .bashrc, which will automatically be called everytime upon opening a terminal

For the latter, you write the following in you terminal: echo 'export SUBJECTS_DIR=/home/developer/FreeSurfer/fs-subjects' >> ~/.bashrc

Otherwise open the file .bashrc in your home directory with any text editor and add the line export SUBJECTS_DIR=/home/developer/FreeSurfer/fs-subjects at the end.

Hope that helps.

Best, Falk

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falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de https://secure-web.cisco.com/1FlD4eMu1iRnV-HvOOVNza4KHxEpb3IRKHdZezUQEyrmz-4... ________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Joanna L Eckhardt jeckhardt@health.ucsd.edu Gesendet: Donnerstag, 12. Mai 2022 04:02:38 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Cannot Locate Newly Completed Recon-all Data

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Dear FreeSurfer Team,

I have exported my SUBJECTS_DIR successfully in the following directory: /home/developer/FreeSurfer/fs-subjects.

When I ran my first recon-all command on subject "sub101-ses-FU," it successfully appeared in my fs-subjects directory along with an fsaverage folder. However, I have ran two other subjects with recon-all and neither have appeared in the fs-subjects directory, even though they successfully completed. In the screenshot below it shows I finished recon-all on subject "sub202-sesFU" but it did not populate in my fs-subjects folder. I cannot find sub202-sesFU anywhere and restarting did not help.

Do you know where my finished subjects might be?

Thank you, Joanna

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Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego