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