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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer