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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