You need to specify the pet input data. See for example the fMRI analysis tutorial here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_freeviewHello 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
No, you will need to as a regressor for the PVR. The way it works is that a design matrix is created from the FSGD. Then when glmfit goes to analyze a particular voxel, it gets the PVR data from that voxel and adds it as a column to the design matrix. So you need to include that column in your contrast matrix.
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?
I don't know. It is your data and you are doing the analysis, so you will know what you are trying to test much better than me!
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:
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On 3/22/17 11:02 AM, miracooloz@gmail.com wrote:
Yes
Sent from my BlackBerry 10smartphone.
Hello,
I am working through the PETsurfer surface based analysis and i have couple of questiona) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness?
mris_preproc is a fronend for mri_concat that makes running mri_concat easier. You can use one or the other but not bothb) 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?
Yes, they use the same underlying code for surface smoothing.c) Can I use mri_surf2surf in place of mris_fwhm? If no, 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.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?
That looks right. You should not need to build a new MC, at least based on that command linee) 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.
Thank youBest,Paul
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