You do not need to rerun; it would generate the same result.

On 5/12/2022 12:50 PM, Joanna L Eckhardt wrote:

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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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________________________________
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

[cid:882a1098-c364-44f5-bee4-8c41b5421a63]

--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego

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