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.
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> Freesurfer@nmr.mgh.harvard.edu
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