External Email - Use Caution
The issue presents in the same way when running "recon-all -long" in Fedora
linux.
As per my message above, modifying "freesurfer/bin/longmc" resolves it.
Best,
Andrea
________________________________
From: fsbuild <fsbu...@contbay.com>
Sent: Tuesday, March 19, 2024 10:13 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bug reporting - longmc: case-sensitive issue in
variable
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.boscu...@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
<longmc_error.log>_______________________________________________
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