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