It worked! Thank you! mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale 251 --mgx 0.01 --o gtmpvcRcc.output
On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > The problem is that --default-seg-merge merges the CC with WM, so you > can't use that option, which means that you'll have to specify the rest > of the default seg merge manually. You can do this with more --replace > args or you can create a file. If you've been able to run mri_gtmpvc > without the current replace, then it will create a replacement file in > the aux folder. Get that, remove the 251 entry, and change the 252-255 > entries to point to 251 > > On 01/29/2016 02:12 PM, Pradeep wrote: > > Unfortunately, that did not fix the problem. > > > > Here is what I did > > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors > > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg # no errors > > > > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 > > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o > > gtmpvcrcc.output > > Loading input t12pet.nii.gz > > done loading input 1 frames > > ERROR: item 251 appears as both source and target seg id in > > replacement list > > > > $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/128_S_0225_v06/mri > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg > > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 > > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o > > gtmpvcrcc.output > > sysname Linux > > hostname > > machine x86_64 > > user > > vgthresh 0.001000 > > nReplace 22 > > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > > 9 avail.processors, using 9 > > Creating output directory gtmpvcrcc.output > > Loading seg for gtm gtmseg.mgz > > Loading seg ctab gtmseg.ctab > > Reading gtmseg.lta > > Replacing 22 > > ERROR: CheckSegTissueType() no entry for seg 192 > > Failed tissue type check > > > > Thank you for looking into this, > > Pradeep > > > > > > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > 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> > > <mailto: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 > >> > > > <mailto: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>> > > > > <mailto: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 > >> > > > <mailto: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>> > > > <tel: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>> <tel: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> > > > > <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> > > > > > > <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>> > > > <mailto: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> > > > <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 > > > > > > > > > > > > > > > _______________________________________________ > > > 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 > > Fax: 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 >
_______________________________________________ Freesurfer mailing list 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.
