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
