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Hi Tim,

I don't think you need to use the `-long` flag when using the `-localGI` flag since that just invokes `mris_compute_lgi` on the lh/rh.pial files.

So after running the longitudinal pipeline to generate lh/rh.pial files, I think you can simply run 
recon-all -s 111002_MR1.long.111002 -localGI

Here, `111002_MR1.long.111002` is assumed to be the dir with the longitudinal outputs.

Alternatively, you could try running `mris_compute_lgi` directly on the pial surfaces of interest.

-Paul

On Thu, Jul 22, 2021 at 3:55 AM Tim Schäfer <ts+ml@rcmd.org> wrote:
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I should maybe add some more info to the last email:

* The error is not subject-specific. I tried for all my subjects, and the error is identical for all of them.
* I am aware of the face that one needs Matlab to run lGI, and it is on the PATH (otherwise the lGI computation for the cross subjects would also fail).
* I know that the error message, on first glance, seems to suggest that there is a syntax error in the recon-all shell script, and that this may suggest that someone messed with it. I strongly believe that this is not the case though, because:
1) FreeSurfer is installed in a directory where only root has write access.
2) The cross subject lGI computation finished successfully this morning.
3) Running 'stat' on the recon-all file shows that it has not been modified after the installation data, more than a year ago.

If you want me to upload subject data, please let me know.

Best,

Tim

> On 07/22/2021 9:43 AM Tim Schäfer <ts+ml@rcmd.org> wrote:
>
> 
> External Email - Use Caution       
>
> 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
>
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--
Tim Schäfer

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