If you are not doing PVC, then the easiest (and most accurate) will be to map the PET to the individual anatomical space, then use mri_segstats with aparc+aseg.mgz as the segmentation to compute the mean in each ROI. If you want to continue with your stream, you can use mri_segstats using --annot fsaverage lh aparc
On 02/17/2016 09:26 AM, Benjamin Spurny wrote:
Hi Doug,
Yes kind of, I am just looking for a way to read out PET data from a surface. I want to do an ROI-based analysis just on brainsurfaces of PET data.
What I did so far is that I coregistered the PET with the MR and used to vol2surf function to project my surface on the fsaverage with each subject.
Is there now a method to read the .mgh files of the surfaces ROI-based using the Desikan atlas?
Currently I am reading them out in Matlab using the .mgh file of my subjects surface and the .annot file from the fsaverage. I just wondered if there is a way to do this in Freesurfer as well?
Best, Benjamin
Am 16.02.2016 20:56, schrieb Douglas N Greve:
Hi Benjamin, do you still have a question about this? I lost the thread so please summarize the problem again. thanks doug
On 02/09/2016 05:01 AM, Benjamin Spurny wrote:
Hello Doug,
Thanks for your answer! I already tried this workflow but basically I am interested in a surface-based analysis. Is it possible by using this workflow to get the any stats.dat just for surface-ROIs?
Best, Benjamin Spurny
On Fr, 29.01.2016, 01:34, Douglas N Greve wrote:
On 01/28/2016 06:50 PM, Pradeep wrote:
Hello Doug,
I have used the gtmseg with --keep-cc flag and the corresponding ctab files showed the labels but the mri_gtmpvc step failed.
Loading seg for gtm gtmseg.mgz Loading seg ctab gtmseg.ctab Reading gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() no entry for seg 192 Failed tissue type check
What is your mri_gtmpvc command line? What is the rest of the terminal output?
My objective is to use the combination of all CC's as a reference region and obtain the PVC results, which would be listed in gtm.stats.dat
It will be best to combine them when running mri_gtmpvc using --replace, eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251 this will cause all segments of the CC to appear to be a single segment (251).
Also, I read in the previous email discussions that the default ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with another ROI as a reference region, would it be OK take a ratio of the ROI's in gtm.stats.dat table.
Yes, or you can spec the new region, eg --rescale 251
Thanks, Pradeep
On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you want to use partial volume correction, then you arebetter off using mri_gtmpvc with the bbr registration, something like
1. To start, run gtmseg --s subject This will take a couple of hours and produces some files needed for GTM PVC (which is used for GTM, MG, RBV). 2. You'd then register the PET to the anatomical withbbregister (probably with --t2 weighting). Make sure to save the output as an LTA (--lta). I usually use the mean TAC as the input. You can do this in parallel with #1.
3. You'd then run mri_gtmpvc, something like mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01--seg gtmseg.mgz --reg reg.lta --default-seg-merge --o gtmpvc.output
PSF is the point-spread FWHM of the scanner; reg.lta is the registration from #2. By default, this will scale by pons. Theoutput will be gtm.stats.dat and gtm.nii.gz. They both basically have the same information. gtm.stats.dat is an easy to read text file. Where each row is an ROI, something like:
9 17 Left-Hippocampus subcort_gm 473 174.083 1.406 0.1216 9 = nineth row 17 = index for RO Left-Hippocampus = name of ROI subcort_gm = tissue class 473 = number of PET voxels in the ROI 174 = variance reduction factor for ROI (based on GLM/SGTM) 1.406 = PVC uptake of ROI relative to Pons 0.1216 = resdiual varaince across voxels in the ROI gtm.nii.gz is a nifti file with each "voxel" being an ROI. Thevalue is the PVC uptake of ROI relative to Pons. These can easily be concatenated together (mri_concat) and used as input to mri_glmfit for group analysis.
On 01/08/2016 04:22 AM, Benjamin Spurny wrote: > Dear Freesurfer experts! > > I am currently working on PET analysis using FS > > I coregistered my PET with the processed MR using bbregister, > transfered it to a surface using mri_vol2surf > and now createt an overlay in freeview with the lh.inflatedand used the > labels from the lh.aparc.a2009s.annot file. > > In freeview i get the corresponding BP value for each vertex now but > is there a way to get a list of vertices with the corresponding BP value > and the corresponding ROI this vertex belongs to? > Or is there a better to do this analyis? > > Many thanks in advance! > > Benjamin > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the personto 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 . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer