On 3/22/17 2:02 PM, miracle ozzoude wrote:
Hello Doug, Thank you for the detailed reply. I do have other questions.
- 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
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_free...
- if both the thickness and pet maps have the same contrast matrices,
can I use one of them as my matrix for multimodal analysis?
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.
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.
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!
Best, Paul
On Wed, Mar 22, 2017 at 1:11 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 3/22/17 11:02 AM, miracooloz@gmail.com <mailto:miracooloz@gmail.com> wrote:Sent from my BlackBerry 10 smartphone. *From: *miracle ozzoude <miracooloz@gmail.com> <mailto: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?Yesb) 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 bothc) 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 lineThank you Best, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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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