Dear Freesurfer experts,
I am trying to run a GLM analysis comparing the difference in the cortical CBF maps between two groups, but I would like to regress out cortical thickness. I read through a post with a similar question (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html), but I am still a little confused and want to confirm the steps of my analysis below:
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1. Compile/smooth CBF data on surface for all subjects. mris_preproc --hemi lh \ --projfrac 0.5 \ --target fsaverage \ --o lh.cbf.00.mgh \ --iv subj1/cbf.mgz subj1/register_pasl.dat \ --iv subj2/cbf.mgz subj2/register_pasl.dat \ ... until subjN
mri_surf2surf \ --hemi lh \ --s fsaverage \ --sval lh.cbf.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.cbf.fwhm10.mgh
2. Compile/smooth thickness data on surface for all subjects. mris_preproc \ --fsgd cbf.fsgd \ --target fsaverage \ --hemi lh \ --meas thickness \ --out lh.thickness.00.mgh
mri_surf2surf \ --hemi lh \ --s fsaverage \ --sval lh.thickness.00.mgh \ --fwhm 10 \ --cortex \ --tval lh.thickness.fwhm10.mgh
3. GLM fit of CBF maps, including thickness as a regressor. mri_glmfit \ --y lh.cbf.fwhm10.mgh \ --fsgd cbf.fsgd \ --pvr lh.thickness.fwhm10.mgh \ --C contrast.ctx \ # where contrast.ctx = "1 -1 0" --surf fsaverage lh \ --cortex \ --glmdir lh.cbf.fwhm10.glmdir \ --eres-save
4. Multiple comparisons correction mri_glmfit-sim \ --glmdir lh.cbf.fwhm10.glmdir \ --perm 1000 1.3 abs \ --cwp 0.05 \ --2spaces \ --bg 35
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I am currently having issues with Step 4; it has been over an hour, and it seems that the command will not finish executing. It is also not outputting any error messages. Whenever I run this analysis using the same parameters but without regressing out thickness, this step takes under five minutes on my machine and returns appropriate results. It seems like I must be doing something wrong, but I'm not sure. Please let me know if there is anything that you would change/add above.
Also, I noticed that you recommended regressing out the overall mean thickness (which you can obtain through mri_glmfit --surf fsaverage lh --osgm --y lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is glm.osgm.lh the mean stratified by class or the overall mean? If I were to include this in my GLM fit, would this be the correct command:
mri_glmfit \ --y lh.cbf.fwhm10.mgh \ --fsgd cbf.fsgd \ --pvr lh.thickness.fwhm10.mgh glm.osgm.lh \ --C contrast.ctx \ # where contrast.ctx = "1 -1 0 0" --surf fsaverage lh \ --cortex \ --glmdir lh.cbf.fwhm10.glmdir \ --eres-save
Thank you for taking a look at this, let me know if you need any other information.
Best, Asim Dhungana
Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b