There is not a flag to do this, but it should be fairly easy. There will be a file called aux/global.gmwmcsf.dat. This has the mean value average over all GM, WM, and CSF voxels (after PVC). You can use this to scale your data like fscalc inputfile.nii.gz div value -o outputfile.nii.gz

You can also use the --scale option when running mri_vol2surf to apply a scaling factor when projecting on to the surface

On 02/14/2017 02:04 PM, Anderson Napolitano wrote:

Hi Experts!

Quick question: is it possible to re-scale intensities relative to the full brain atlas? Details: Per step 3 of the following tutorial:

https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer

I wanted to re-scale the the intensities relative to the full brain atlas. The command:

--no-rescale

removes scaling relative to the Pons and the command:

--rescale <Ids>

rescales the intensities relative to the region determined by Ids. Would listing all the regions on the --rescale command be the right approach to rescale the intensities relative to the atlas? If so, how do I determine which Ids is which?

Thank you in advance!

-Anderson

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