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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- 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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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