Did you source the freesurfer enviroment?
On 6/11/2021 4:28 AM, Juan Felipe Quinones Sanchez wrote:
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Dear Freesurfer team,
I am new to Freesurfer. I installed it on my WSL (ubuntu 18.04) following the instructions at: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_wsl https://secure-web.cisco.com/19NPylFTZm62HJK1A_0s-94uhHZebqqpw9Sitxzpx_bTWotvZkXBlcvKWyOUSXTB6paCe4qC2IKZQ4CWTUhQ1G0BvGwI6KzDF5Fe4HfoRf8Lu9bGkUC2PrUfIYg_rZUHn0GuLqyAtOS2rjah1Ak0VKLY-BxYv1i--zeaPaEFk3q0VDl3-UwLfWBCgzZfSl-PlacP4JE_W9J2Mz4H3ZNL9awvAwecXspklIC0TevTuPUy0W58HCZ7_sB6cY4rSrwy_6sZ_rIJqILd88Rypnkjrmg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_wsl. 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 (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67057.html https://secure-web.cisco.com/1H4D7loaV8UEB6OJaKKwdNSc3rqTSamNp7b7KUKBFFvTH3CqsUAITGhVJ86H2Xz-XtBnb6rj8GblPIO1WDG65b9o15sEDfgIiX9vdPudWyCFt4mZn6-bS7tHWwYGyclswXGu8MnO8ttvY1t_WYnd1xsG5BqEfzsUOTs2frM2fWvDTNXNZ-dSvgQiang74hsQnYrixN6i_RI5xOhU6fulR3bHg1uH8JraC2ieV2DvW6jkgaxfzlGi4MDENxk4yr1UjMEw1oOM3IDzgdcztxZnqlQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67057.html) 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 (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.freesurfer.net/pub/dist/freesurfer/dev_binaries/centos6_x86_64/r... https://secure-web.cisco.com/1rA78FG6F2-U9A7bR00W9v_d5uE-voxX7qbpwkAvn5xBbokI_skGYxiPH81ncanYmZGOE58SBnyqcvgVbGJYdIdyS2b8d2KW75DmdqkGhtAGUQ9FVRCMfulYvebFvWNKYgaCJ2b72fj8QJsCVElyFv9P1bluG2qYNuxSY3pyw2dYG_MwGwqIiYKrHaG2RmvuI6o0mBC7qaKo3iRjx1M32jiEgd3CuXwYvPZobFpXNoo8fDe3B6tCFGFHbk_4YJ8W1o7wULav3CSwaok4dT3TBYQ/https%3A%2F%2Fwww.freesurfer.net%2Fpub%2Fdist%2Ffreesurfer%2Fdev_binaries%2Fcentos6_x86_64%2Frecon-all) 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
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