RE: [Freesurfer] recon-all error

Jenni Pacheco Mon, 09 Oct 2006 14:19:24 -0700

It appears that you are still having a problem because there are spaces in the name of your dicom file:
mri_convert /root/Cath/ADULT /usr/local/freesurfer/subjects/Cath01/mri/orig/001.mgz
unknown file type for file /root/Cath/ADULT

Its looking to convert the file /root/Cath/ADULT – which it can’t identify as a dicom because it’s actually named ADULT 14-0005-0001-0001.dcm

There may be some more fixes you could introduce to your recon-all script, but you could also try renaming your dicoms to something without a space and use those – that might be easier.

Jenni

From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Anil Roy
Sent: Monday, October 09, 2006 5:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all error

Thanks a lot. recon-all runs after applying the fix. However, I seem to have run into a different error. Here is the output after running recon-all on the same dcm file:

# recon-all -i /root/Cath/ADULT\ 14-0005-0001-0001.dcm -subjid Cath01 -sd /usr/local/freesurfer/subjects

INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux dhcp-129-105-146-165.speech.northwestern.edu 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux
WM removal version
/usr/local/freesurfer/subjects/Cath01

mri_convert /root/Cath/ADULT /usr/local/freesurfer/subjects/Cath01/mri/orig/001.mgz

mri_convert /root/Cath/ADULT /usr/local/freesurfer/subjects/Cath01/mri/orig/001.mgz
unknown file type for file /root/Cath/ADULT
Linux dhcp-129-105-146-165.speech.northwestern.edu 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Mon Oct 9 16:01:02 CDT 2006

The files I'm using are the T1 weighted anatomical images from a 3T Seimens scanner. The only operation done on the files prior to the recon-all procedure is to rename them.

Thanks,

Anil.

On 10/6/06, Nick Schmansky <[EMAIL PROTECTED]> wrote:

Anil,

It does seem that the recon-all script does not handle input files
containing spaces.  However, you can fix your recon-all script by
editing it and replacing the 'case "-i"' section with this:

    case "-i"
      if( $#argv < 1) goto arg1err;
      set InputVol = "$argv[1]"; shift;
      if(! -e "$InputVol") then
        echo "ERROR: cannot find $InputVol"
        exit 1;
      endif
      if(! -r "$InputVol") then
        echo "ERROR: $InputVol exists but is not readable"
        exit 1;
      endif
      set InVolDir  = `dirname  "$InputVol"`;
      set InVolBase = `basename "$InputVol"`;
      pushd $InVolDir > /dev/null
      set InVolDir = `pwd`;
      popd > /dev/null
      set InputVol = "$InVolDir/$InVolBase";
      set InputList = ($InputList "$InputVol");
      set DoConvertInput = 1;
      breaksw

The change is the inclusion of double-quotes "" on certain variables.

This fix will appear in the next stable release.

Nick

On Fri, 2006-10-06 at 16:25 -0500, Anil Roy wrote:
> Hello all,
>
> I get the following error when I feed in a dicom file into recon-all.
> The dicom file is in a directory with 159 other dcm files. Can you
> please tell me how to rectify this or what the source of the error
> is.
>
> [EMAIL PROTECTED] freesurfer]# recon-all -i /root/Cath/ADULT\
> 14-0005-0001-0001.dcm -subjid E001 -sd /usr/local/freesurfer/subjects
> -all
> set: Variable name must begin with a letter.
>
> Thanks,
>
> Anil.
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] recon-all error

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