mri_glmfit will not generate a pcc file with --pvr. I think I just did not get around to adding support for this. What about the sig does not look right? You can often get funny looking maps because each voxel is a different design matrix.
On 05/09/2017 03:15 PM, Martin Juneja wrote: > 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 X001Male36 > InputX003Male29 > InputX004Male39 > 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 <mailto: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> > <mailto: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> > > > <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> > > <mailto: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> > > <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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <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> > > <http://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/> > > <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> > <mailto: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> > > > <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> > > <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 > <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:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > 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
