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 >>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>>> wrote: >>>> >>>> >>>> If you want to use partial volume correction, then you are >>>> better >>>> 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 with >>>> bbregister >>>> (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. The >>>> output >>>> 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. The >>>> value >>>> 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.inflated >>>> and >>>> 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 >>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@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.edu >>>> <mailto: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 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 . 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 >>> gr...@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 > gr...@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 -- NEUROIMAGING LABs (NIL) - PET & MRI & EEG & Chemical Lab Department of Psychiatry and Psychotherapy, MEDICAL UNIVERSITY OF VIENNA Währinger Gürtel 18-20, A-1090 Wien, Austria http://www.meduniwien.ac.at/neuroimaging/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
