Hello Doug, Thank you for the detailed reply. I do have other questions. 1) Can you confirm if this is the correct use of mris_preproc for Uncached PET data. mris_preproc --fsgd your.fsgd --target fsaverage --hemi lh --meas Pet --out lh.your.pet.00.mgh. This modification was made from the thickness thickness data. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
2) if both the thickness and pet maps have the same contrast matrices, can I use one of them as my matrix for multimodal analysis? 3)What if they don't share similar contrast matrices, Can i still perform multimodal analysis? This is because contrast matrices are based on regressors and class in fsgd files. Best, Paul On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 3/22/17 11:02 AM, miracoo...@gmail.com wrote: > > > > Sent from my BlackBerry 10 smartphone. > *From: *miracle ozzoude <miracoo...@gmail.com> <miracoo...@gmail.com> > *Sent: *Tuesday, March 21, 2017 7:41 PM > *To: *Douglas N Greve > *Subject: *PETsurfer surface based analysis > > Hello, > I am working through the PETsurfer surface based analysis and i have > couple of question > a) Since the procedure is the same as surface based analysis for cortical > thickness except mri_vol2surf, Can I use the procedure for thickness? > > Yes > > b) What is the difference between mris_preproc and mri_concat. If I use > mris_preproc, do I also need to use mri_concat? Also, can I use > mris_preproc instead of mri_concat? > > mris_preproc is a fronend for mri_concat that makes running mri_concat > easier. You can use one or the other but not both > > c) Can I use mri_surf2surf in place of mris_fwhm? If no, why? > > Yes, they use the same underlying code for surface smoothing. > > d) While researching PETsurfer surface based analysis in the forum, I came > across multiple trends that used the "--projfrac" flag in both mri_vol2surf > command and mris_preproc command. At what stage should I include this flag > and why? > > At which the time you run the program. If you are using mri_vol2surf prior > to mris_preproc, then you would not include it in mris_preproc. > > e) If I want to perform a multimodal analysis using thickness&PET or > Surface area&PET, Can anyone confirm if this is the correct steps. > > - Perform surface base analysis for cortical thickness from step 1 > (mris_preproc) to correction for multiple comparison > - Perform PET surface based analysis from step 1 (gtmseg) to step 5. > While conducting mri_glmfit, include the smoothed thickness map > (?h.thickness.10B.mgh) as pvr (per vertex regressor) > - e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr > lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir > pvr.lh.pet.thickness.glmdir > - Lastly, build a new monte carlo correction for multiple comparison. > > That looks right. You should not need to build a new MC, at least based on > that command line > > Thank you > Best, > Paul > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > 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 . 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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