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 >>>>> <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 -- 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
