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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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