Hi Fleur,
It’s definitely running with tcsh. Can you provide a bit more context for the
error? Like is there any terminal output preceding it?
Andrew
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fleur Warton
<fleur.war...@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, May 20, 2020 at 6:13 AM
To: fsbuild <fsbu...@contbay.com>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer: infant_recon_all error
External Email - Use Caution
Hi,
Thanks for the reply! The output for 'file' was tcsh. I switched to tcsh (just
in that session) but got the same error when running infant_recon_all
if: Expression Syntax
Kind regards,
--
Fleur Warton
Postdoctoral Research Fellow
Division of Biomedical Engineering
Faculty of Health Sciences
University of Cape Town
On Wed, May 20, 2020 at 11:42 AM fsbuild
<fsbu...@contbay.com<mailto:fsbu...@contbay.com>> wrote:
Hello Fleur,
You should be able to do,
$ file `which infant_recon_all`
... and the output should tell you if it it is a csh script, a Bourne shell
script, a binary, etc.
Unless you explicitly made csh or bash your default shell, then at the dollar
sign prompt the default shell in Ubuntu is "dash" and not bash or Bourne shell.
If the file command reports it's a Bourne shell then it might be a bash
script. Or a bash script with a hash bang line of /bin/sh will run using dash
shell on Ubuntu and can exit with that error on bash syntax/grammar. You can
eliminate that possibility by first running bash, and then the script,
$ bash
$ infant_recon_all --s SUBJ --age AGE
(with I presume arguments substituted for SUBJ and AGE)
- R.
Fleur Warton<mailto:fleur.war...@gmail.com>
May 20, 2020 at 04:05
External Email - Use Caution
Hi,
I recently installed the Infant FreeSurfer package. When I try to run
infant_recon_all (specific command: infant_recon_all --s SUBJ --age AGE)
I get the error
if: Expression Syntax
I tried switching shells from bash to tcsh but got the same error.
The FreeSurfer version is freesurfer-infant-20200205
My platform is Ubuntu 18.04
Any suggestions how to fix this?
Kind regards,
Fleur
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
