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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