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-bounces@nmr.mgh.harvard.edu> on behalf of Fleur Warton <fleur.warton@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, May 20, 2020 at 6:13 AM
To: fsbuild <fsbuild@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 <fsbuild@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

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

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