Hi Doug,
Here was my original question (we haven't communicated outside of this thread):
I've recently run into a case the gtmstats uptake (reference region:
cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing
the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and
aux/seg.nii.gz, the values are closer to 1, as expected. This is using
Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas
why we get such bad values from the GTM method?
Then you asked, "What is the value for cerebellum in those three scenarious
(gtm, no pvc, and mgx)?"
So I added the uptake values for the cerebellum to the original table, which
I've pasted below. Let me know if there's anything else you need.
Thanks!
Ryan
vol | psf | roi | gtmstats_uptake |
region_mean
-----------------------+-------+-------------------------+-------------------+---------------
input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 |
1.226
input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 |
1.0834
input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex | 0.981 |
0.994237
input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 |
1.03552
mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 |
1.00685
mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 |
0.887616
input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 |
1.19702
input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.47 |
1.05779
input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex | 0.984 |
0.970736
input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 |
1.01104
mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 |
0.915328
mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.47 |
0.809017
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Wednesday, April 1, 2020 10:16 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine
Can you include previous emails so that I have some context as to what you are
asking?
On 4/1/2020 9:18 AM, Eckbo, Ryan wrote:
Here's a table with the cerebellum uptake values included -- let me know if you
need more information.
vol | psf | roi | gtmstats_uptake |
region_mean
-----------------------+-------+-------------------------+-------------------+---------------
input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 |
1.226
input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 |
1.0834
input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex | 0.981 |
0.994237
input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 |
1.03552
mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 |
1.00685
mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 |
0.887616
input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 |
1.19702
input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.47 |
1.05779
input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex | 0.984 |
0.970736
input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 |
1.01104
mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 |
0.915328
mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.47 |
0.809017
Thanks!
Ryan
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, March 11, 2020 10:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine
What is the value for cerebellum in those three scenarious (gtm, no pvc, and
mgx)?
On 3/10/2020 12:37 PM, Eckbo, Ryan wrote:
Hello experts,
I've recently run into a case the gtmstats uptake (reference region:
cerebellum) for the pericarlcarine ROI's are as low as 0.40,
however computing the voxel wise mean using input.rescaled.nii.gz and
mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1,
as expected:
| vol | psf | roi | gtmstats_uptake |
mean_uptake |
| --------------------- | --- | -------------------- | --------------- |
----------- |
| input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 |
1.226… |
| input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 |
1.083… |
| input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 |
1.197… |
| input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 |
1.058… |
| mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 |
1.007… |
| mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 |
0.888… |
| mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 |
0.915… |
| mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 |
0.809… |
This is using Freesurfer 6.0, and the PET to anatomical registration looks fine.
Any ideas why we get such bad values from the GTM method?
Thanks for any help,
Ryan
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