To use the PVR, you need to create a stack of the measures that you want
to use (eg, lGI). This will be the same size as the stack you want to
correlate with. Eg, if you use mris_preproc to create a thickness stack,
you would use the same command to create the lGI stack. Create your FSGD
file as normal, but when you create your contrast file, make sure to add
a column to handle the per-vertex regressor. Eg, if you have two groups,
then you would create a contrast [0 0 1] to test for the effect of the
PVR. When you run mri_glmfit, just add --pvr lgi.mgz



On 04/27/2017 06:13 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I did not find --help option very helpful here and also I could not
> find much help from the previous FreeSurfer posts. Could you please
> share more details here e.g. how to set up fsgd and contrast file and
> how to run mri_glmfit command here (e.g. what inputs should be
> provided here?).
>
> I am basically interested in correlating volume and gyrification
> regressing out the effect of age and gender. I already have
> lh.pial_lgi and lh.volume files saved in 'surf' directory of each subject.
>
> Thanks.
>
> On Thu, Apr 27, 2017 at 8:42 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     You have to use the --pvr option to mri_glmfit. Run it with --help to
>     get more info and write back if you still have questions
>
>
>     On 04/26/2017 08:33 PM, Martin Juneja wrote:
>     > Hello FreeSurfer experts,
>     >
>     > I came across a paper:
>     >
>     http://www.sciencedirect.com/science/article/pii/S0166432815001837
>     <http://www.sciencedirect.com/science/article/pii/S0166432815001837>
>     > where correlation maps between volume and gyrification are reported.
>     >
>     > I am familiar with GLM in FreeSurfer i.e. correlating behavioral
>     > measures with volume and gyrification but I was wondering how to
>     > correlate structure measures with each other e.g. volume and
>     gyrification.
>     >
>     > I would really appreciate any help.
>     >
>     > Thanks.
>     >
>     >
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358 <tel:617-724-2358>
>     Fax: 617-726-7422 <tel:617-726-7422>
>
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>     <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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