Hello FSL team,
I apologize for such a basic question, but I have searched the listserv archives and the VBM FAQs for an answer and don't find it.
I have used FSL-VBM using the standard and recommended settings (according to the VBM User Guide) to generate my template-registered grey matter images. In reading through helpful guides to VBM (e.g. Douglas Greve's http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf), I find references to using VBM to measure tissue concentration or density, and then using the Jacobian determinant to measure volume of the same structural images. Using the standard VBM settings, as I understand it the output of randomise reflects the difference in tissue density or concentration between groups. If I want to instead output the volume differences between groups, would I run
fslvbm_3_proc on the Jacobian warp field instead of on the warped FA image? If I understand the file name structure correctly, this would mean running fslvbm_3_proc on {identifier}_FA_to_target_warp.nii.gz instead of {identifier}_FA_to_target.nii.gz.
Is this correct? If not, how can I use VBM to measure volume instead of tissue density?
Thanks ever so much for the help,
Andrew Faust
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