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 <greve@nmr.mgh.harvard.edu> wrote:

On 3/22/17 11:02 AM, miracooloz@gmail.com wrote:

Sent from my BlackBerry 10 smartphone.

From: miracle ozzoude <miracooloz@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
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