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Great, thank you for the confirmation!
All my best,
Joanna
--
Joanna Eckhardt
Neurosciences Graduate Program
University of California, San Diego
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Thursday, May 12, 2022 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de>
<falk.luesebr...@med.ovgu.de><mailto:falk.luesebr...@med.ovgu.de>
Sent: Thursday, May 12, 2022 2:27 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cannot Locate Newly Completed Recon-all Data
External Email - Use Caution
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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Universitätsklinik für Neurologie
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Telefon: +49-391-6117-512
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________________________________
Von:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
im Auftrag von Joanna L Eckhardt
<jeckha...@health.ucsd.edu><mailto:jeckha...@health.ucsd.edu>
Gesendet: Donnerstag, 12. Mai 2022 04:02:38
An: freesurfer@nmr.mgh.harvard.edu<mailto: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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