I think I see the problem. When you run gtmseg, you need to add --keep-cc. You can rerun it using the previous command line, but add --keep-cc and --no-xcerseg. The second option tells it not to redo the extracerebral segmentation (which won't change with CC)
On 01/29/2016 11:21 AM, Pradeep wrote: > Thank you for the response. > > Here is my full command log with error > > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > Loading input t12pet.nii.gz > done loading input 1 frames > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $ > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc > cd /analysis/software_test/fs6pvc/******/mri > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o > gtmpvccc.output > sysname Linux > hostname server > machine x86_64 > user user > vgthresh 0.001000 > nReplace 18 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > 9 avail.processors, using 9 > Creating output directory gtmpvccc.output > 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 > > > Thanks, > Pradeep > > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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> > <mailto: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> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <mailto: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 > <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 > > > > > _______________________________________________ > 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
