Re: [Freesurfer] Reading values from overlays with PETcoreg

Dear Doug, Is it possible to use BP SUVR PET that have been registered to T1 for this gtmseg workflow? You mentioned that the mean TAC should be used as the input. 2 quick questions: What's mean TAC and why? Thanks. Best Wishes, Elijah ___ Freesurfer

Re: [Freesurfer] Reading values from overlays with PETcoreg

No, not yet, though I recently had a need to do the same thing. It is pretty easy to do though. If you run mri_gtmpvc with --save-input, it will create a file called input.rescaled.nii.gz. Then you can run mri_segstats --i input.rescaled.nii.gz --seg aux/seg.nii.gz --ctab aux/seg.ctab

Re: [Freesurfer] Reading values from overlays with PETcoreg

Hello Doug, I was wondering if there is a flag in the command to obtain the SUVRs for the same ROIs with out partial volume correction so that it would be easier to compare. Thanks, Pradeep On Fri, Jan 29, 2016 at 1:30 PM, Pradeep wrote: > It worked! Thank you! >

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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 wrote: > The problem

Re: [Freesurfer] Reading values from overlays with PETcoreg

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 >

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

Re: [Freesurfer] Reading values from overlays with PETcoreg

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

[Freesurfer] Reading values from overlays with PETcoreg

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