Dear Victoria,
to obtain the volume in litres of a masked region, you can use the
following:
spm_summarise('mask.nii','all','litres')
If you want to restrict the computation of the volume to intracranial
regions, you can type:
spm_summarise('mask.nii',fullfile(spm('Dir'),'tpm','mask_ICV.nii'),'litres')
that here uses a mask provided in SPM12.
Best regards,
Guillaume.
On 19/01/15 23:08, Victoria Villalta wrote:
> Dear SPMers,
> I have run a series of first level analysis and I am trying to find a quick method to detect "crappy" masks. So far I have created conjunction images with my grey matter binary template and my resulting binary masks and was counting {sum(output3(:))} the amount of voxels in the resulting image.
> This method is not giving me the info that I am looking for as the mask that is partially ok gives me an answer of 5346 and the bad mask gives me an answer of 5394. It's clear that the answer I get from {sum(output3(:))} it is not reflecting the number of "white" voxels.
> Are you aware of any other method I could use to have a count of number of voxels in masks that I could apply to have gross cutoff information of very bad ones?
> Thanks tons!
> V
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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