External Email - Use Caution
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-20200205My platform is Ubuntu 18.04 Any suggestions how to fix this? Kind regards, Fleur
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 fleur.warton@gmail.com May 20, 2020 at 04:05
External Email - Use CautionHi,
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.commailto: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 Wartonmailto:fleur.warton@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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Fleur Warton -
fsbuild -
Hoopes, Andrew