Dear Prof Schwarz,


Please can you help me with the script for computing the grey matter volumes for specific regions of interest found in  MCALT atlas. 

I have done the following steps:

1./ Segmented and normalized the images to the MCALT space using the matlab script you provided with the atlas (Thank you very much).

2./ The grey matter probability maps are smoothen using 6mm FWHM gaussian kernel.

3./ I have transformed the MCALT atlas into the native space of the image by using normalization parameters for transforming the image to MCALT space.

Kate

Kate,
If you have already transformed the atlases into the native space, then GM volumes are computed by summing the voxels in the c1*.nii segmentation maps within each atlas region. You then multiply by the volume of each voxel to convert the units mm^3. Sorry, I do not have code that I can provide for this, but it seems like you have already done the parts of it that are relatively more difficult. Eventually I plan to include code to compute GM volumes but this is not available yet and I do not have an ETA.
Best regards,
Chris

Thanks Dr Schwarz for the information.

Kate

Kate,
Today's 1.4 release now includes code that computes regional GM volumes and TIV measurements.
Best regards,
Chris