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 m
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 --avgwfvol
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!
> mri_gtmpvc --i t12pet.nii.gz
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
--ann
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
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 an
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 01/2
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 is that --default-seg-merge
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 c
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
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 wro
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
do
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
> E
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
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 reg
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.
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