External: Increase caution when handling links and attachments.

On Ubuntu linux the default shell may still be “dash” and not the “bash” shell. Dash cannot parse all bash scripting, so type “bash” or try setting “bash” to be your default shell and then run commands.

- R.

On Mar 19, 2024, at 22:17, Boscutti, Andrea <Andrea.Boscutti@uth.tmc.edu> wrote:

External Email - Use Caution

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
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