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Ok good to hear!  Thanks for the update.

-Paul

On Fri, Jul 23, 2021 at 3:22 AM Tim Schäfer <ts+ml@rcmd.org> wrote:
        External Email - Use Caution       

Running mris_compute_lgi directly works, thanks for the help!

Tim

> On 07/23/2021 8:59 AM Tim Schäfer <ts+ml@rcmd.org> wrote:
>
> 
> External Email - Use Caution       
>
> Hi Paul,
>
> thanks for the suggestion. Leaving the -long part out like this:
>
>     recon-all -s 111002_MR1.long.111002 -localGI
>
> ...gives the following error instead:
>
> ERROR: Are you trying to run or re-run a longitudinal time point?
>        If so, please specify the following parameters:
>
>        \' -long <tpNid> <templateid> \'
>
>        where <tpNid> is the time point id (SAME as cross sectional
>        ID) and <templateid> is the ID created in the -base run.
>        The directory <tpNid>.long.<templateid> will be created
>        automatically or used for output, if it already exists.
>
> I will try your second suggestion and run `mris_compute_lgi` directly.
>
> Thanks,
>
> Tim
>
> > On 07/22/2021 9:43 PM Paul Wighton <paul@corticometrics.com> wrote:
> >
> > 
> > External Email - Use Caution       
> >
> > 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:
> >
> > >         External Email - Use Caution
> > >
> > > 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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> --
> Tim Schäfer
>
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--
Tim Schäfer

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