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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, March 11, 2020 10:01 AM
To: freesurfer@nmr.mgh.harvard.edu <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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