Can you tar up the output folder and send it to me at our file drop?

https://gate.nmr.mgh.harvard.edu/filedrop2

Thank you Doug. I am trying to perform pvc for my pet data based on the tutorial however, I keep getting this error: 

" mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output

Loading input C6_01_001_140813_PET_AV45_coreg_avg.nii.gz

  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $

setenv SUBJECTS_DIR /net/synapse/nt/paul/Analysis

cd /net/synapse/nt/paul/Analysis

mri_gtmpvc --i C6_01_001_140813_PET_AV45_coreg_avg.nii.gz --reg C6_01_001_140813_PET_AV45_coreg_avg.reg.lta --psf 6mm --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 0.01 --o C6_01_001_140813.gtmpvc.output

sysname  Linux

hostname neuron2.sri.utoronto.ca

machine  x86_64

user     paul

vgthresh   0.001000

nReplace   18

0.0000 0.0000 0.0000 0.0000 0.0000 0.0000

24 avail.processors, using 1

Creating output directory C6_01_001_140813.gtmpvc.output

Loading seg for gtm /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.mgz

Loading seg ctab /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.ctab

Reading /net/synapse/nt/paul/Analysis/C6_01_001_140813/mri/gtmseg.lta

Replacing 18

Pruning ctab

ERROR: CTABpruneCTab(): ctab does not have segid 192

Checking tissue type

Segmentation fault"

Step 1 and 2 were successful. Please can you tell me what is wrong. Thanks

Best, 

Paul 

On Wed, Mar 22, 2017 at 3:07 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

On 3/22/17 2:02 PM, miracle ozzoude wrote:

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

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_freeview

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?

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> 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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