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 nicks@nmr.mgh.harvard.edu 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.

[root@dhcp-129-105-146-217 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

I went for the renaming route. Everything seems to be running fine now.

Thanks,

Anil.

On 10/9/06, Jenni Pacheco jpacheco@nmr.mgh.harvard.edu wrote:

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:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *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* nicks@nmr.mgh.harvard.edu 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.

[root@dhcp-129-105-146-217 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