Dear Dr. Greve, I created two stacks: one with volume and the other with LGI using mris commands as following:
mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas volume --out Corr_CV_LGI/lh.vol.mgh mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas pial_lgi --out Corr_CV_LGI/lh.LGI.mgh Then I smoothed the data using: mri_surf2surf --hemi lh --s fsaverage --sval Corr_CV_LGI/lh.vol.mgh --fwhm 10 --cortex --tval Corr_CV_LGI/lh.vol.10.mgh mri_surf2surf --hemi lh --s fsaverage --sval Corr_CV_LGI/lh.LGI.mgh --fwhm 10 --cortex --tval Corr_CV_LGI/lh.LGI.10.mgh Finally I ran glmfit command as following: mri_glmfit --y Corr_CV_LGI/lh.vol.10.mgh --fsgd CV_LGI.fsgd dods --C Corr-VL-cor.mtx --surf fsaverage lh --cortex --glmdir Corr_CV_LGI/lh.VL.glmdir --pvr Corr_CV_LGI/lh.LGI.10.mgh My fsgd file looks like this: GroupDescriptorFile 1 Class Male Class Female Variables Age Input X001 Male 36 Input X003 Male 29 Input X004 Male 39 etc. and my contrast file (Corr-VL-cor.mtx) is: 0 0.5 0.5 0 1 (I am interested in regressing out the effect of age and gender). These steps do not give me any error but somehow (i) I do not get pcc.mgh (partial correlation between volume and LGI measures) file and (ii) sig.mgh file also does not seem correct. Could you please help me in figuring out the error or where I am doing wrong? Thanks. On Fri, Apr 28, 2017 at 3:19 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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:freesur...@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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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