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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