External Email - Use Caution
Dear Freesurfer team,
I am new to Freesurfer. I installed it on my WSL (ubuntu 18.04) following the instructions at: https://secure-web.cisco.com/19NPylFTZm62HJK1A_0s-94uhHZebqqpw9Sitxzpx_bTWot.... I believe that the installation was successful because I get documentation whenever I type a function on the command line. I wanted to run recon-all on a T1 image using the following call:
$FREESURFER_HOME/bin/recon-all -s subx -i $t1_img -all
where $t1_img = /mnt/c/Users/...../t1.nii.gz
Unfortunately I got the following error:
rca-config: Command not found.
I read a thread (https://secure-web.cisco.com/1H4D7loaV8UEB6OJaKKwdNSc3rqTSamNp7b7KUKBFFvTH3C...) addressing this topic and followed the suggested solution. I typed everything manually. I also ran the code directly from the console and from a bash script, both with the $t1_img variable and the original file path but the error persists.
I found this code (https://secure-web.cisco.com/1rA78FG6F2-U9A7bR00W9v_d5uE-voxX7qbpwkAvn5xBbok...) supposedly running recon-all and there is a line where the command "rca-config" is used. However, it seems to be not recognized even though the file is indeed located at $FREESURFER_HOME/bin/.
I would appreciate any sort of guidance.
Thank you,
Juan