External Email - Use Caution
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 1For 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 $ConcatLtas`Best,Andrea<longmc_error.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
The issue presents in the same way when running "recon-all -long" in Fedora linux.
As per my message above, modifying "freesurfer/bin/longmc" resolves it.
Best,
Andrea ________________________________ From: fsbuild fsbuild@contbay.com Sent: Tuesday, March 19, 2024 10:13 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Bug reporting - longmc: case-sensitive issue in variable
External: Increase caution when handling links and attachments.
On Ubuntu linux the default shell may still be “dash” and not the “bash” shell. Dash cannot parse all bash scripting, so type “bash” or try setting “bash” to be your default shell and then run commands.
- R.
On Mar 19, 2024, at 22:17, Boscutti, Andrea Andrea.Boscutti@uth.tmc.edu wrote:
External Email - Use Caution
Hello FreeSurfer Developers, When attempting to run "recon-all -long" in subjects with multiple T1 inputs, I get the following error when "longmc" is run:
concatLtas: Undefined variable. if: Expression Syntax. Command exited with non-zero status 1
For the entire log, see attached "longmc_error.log".
The following change at line 188 of "freesurfer/bin/longmc" fixes it (case-sensitive issue in "$concatLtas"):
set ud = `UpdateNeeded $origvol $CrossList $concatLtas --> set ud = `UpdateNeeded $origvol $CrossList $ConcatLtas`
Best,
Andrea <longmc_error.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr..mgh.harvard.edu https://secure-web.cisco.com/1CxZQT6CEbDxyBag0SXHhWAt2Edm7xMLYpDEVuBZBnWyblY...
freesurfer@nmr.mgh.harvard.edu
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Boscutti, Andrea -
fsbuild