Re: [Freesurfer] Bug reporting - longmc: case-sensitive issue in variable

Hi Andrea,

Thanks for finding this and the fix. I created a pull request that fixes this in our dev version.

Best, Martin

On 20. Mar 2024, at 03:17, Boscutti, Andrea Andrea.Boscutti@uth.tmc.edu wrote:

Hello FreeSurfer Developers, When attempting to run "recon-all -long" in subjects with multiple T1 inputs, I get the following error when "longmc" is run:

concatLtas: Undefined variable. if: Expression Syntax. Command exited with non-zero status 1

For the entire log, see attached "longmc_error.log".

The following change at line 188 of "freesurfer/bin/longmc" fixes it (case-sensitive issue in "$concatLtas"):

set ud = `UpdateNeeded $origvol $CrossList $concatLtas --> set ud = `UpdateNeeded $origvol $CrossList $ConcatLtas`

Best,

Andrea <longmc_error.log>