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Dear FreeSurfer experts,
I am trying to compute local lGI in FreeSurfer 6 for a subject that has undergone longitudinal processing.
In this example, the longitudinal base subject folder (with the long template recon-all output for that subject) is called "111002" and the folder with the data for timepoint 1, for which I would like to compute lGI now, is called "111002_MR1.long.111002". So I run the following command:
recon-all -long 111002_MR1.long.111002 111002 -localGI
The only output, after less than a second, is:
Unmatched '"'.
Then the script terminates and I am back at the shell. Any thoughts on this or ideas?
I have successfully computed local lGI for the cross subjects on the same computer, it finished this morning (using the command 'recon-all -s $CROSS_SUBJECT -localGI'). So the recon-all command in general seems to work, the error is specific to the lgi long command it seems.
Here is some system info:
cat $FREESURFER_HOME/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
uname -a
Linux lxsrv2 5.8.0-59-generic #66~20.04.1-Ubuntu SMP Thu Jun 17 11:14:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
All the best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany