Thank you! I ran the development version of the mri_glmfit-sim command on my data, and it did not crash and seems to give reasonable outputs (smaller clusters disappear after correction). Whenever your tests are done, it will be good to know if they confirm that everything is working.
Best, Asim ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, February 21, 2022 6:29 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness I just updated the code to accept PVRs. I'm not sure what I have to do to test it; I guess I need to run the null test like I did for the non-PVR version. This will take a while. In the mean time, can you download the development version and just try it on your data to see if it crashes or gives results that don't seem to make sense? You'll have to wait until the development version is updated (probably tomorrow). On 2/17/2022 5:22 PM, Dhungana, Asim wrote: Hello Doug, just following up on my questions below on how/if I can correct for multiple comparisons with PVR. Thanks again. Best, Asim ________________________________ From: Dhungana, Asim <adhung...@mgh.harvard.edu><mailto:adhung...@mgh.harvard.edu> Sent: Monday, February 14, 2022 11:45 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness OK, I see. How would you recommend correcting for multiple comparisons if the perm option does not work with PVR? Also, are you saying that I should only use the glm.osgm.lh/eres.mgh file as a pvr argument? Does this look correct: mri_glmfit \ --y lh.cbf.fwhm10.mgh \ --fsgd cbf.fsgd \ --pvr glm.osgm.lh/eres.mgh \ --C contrast.ctx \ # where contrast.ctx = "1 -1 0" --surf fsaverage lh \ --cortex \ --glmdir lh.cbf.fwhm10.glmdir \ --eres-save Best, Asim ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Sunday, February 13, 2022 5:29 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness Re: long run time. Sorry, permutation will not work with PVR. Re: mean thickness. Use the eres.mgh from you osgm analysis instead of the raw thickness map (lh.thickness.fwhm10.mgh) On 2/8/2022 4:12 PM, Dhungana, Asim wrote: 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: --- 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 --- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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