Dear Wi Hoon,
On Fri, 21 Oct 2016 15:49:01 +0100, WH Jung <[log in to unmask]> wrote:
>Dear Dr. Christian Gaser,
>
>Thank you so much for answering my earlier question about a customized template.
>
>I also have some questions abut extracting ROI values using CAT12, though CAT12 extracts ROI values from different volume and surface-based atlas maps which is provided with CAT12 (i.e., 3 atlases [hammers, neuromorphometrics, and lpba 40 atlases] for volume-based maps; 2 atlases [aparc_DK40 and aprac_a20009s] for surface-based maps]).
>
>1) The “catROI_*.xml” contains several ROI values. Could you explain the meaning of each label, particularly the meaning of each prefix, V*, I*, and T*? Is it right to use V* values for statistical analysis?
V - Volume
I - Intensity (useless)
T - Thickness
However, you can try the new Analyze ROI function that will use an existing SPM design and applies the same statistical tests and controls for the same nuisance parameters. Here, volumes (mainly for GM) and surface measures (e.g. thickness, gyrification, fractal dimension) can be analyzed automatically.
>
>2) As mentioned above, CAT12 does not use the same atlas when extracting ROI values from volume (gray and white matter volumes) and surface-based maps (cortical thickness) respectively, which makes difficult to directly compare/combine ROI values extracted from two different module maps. Is there any way to extract ROI values from the same atlas for both volume and surface-based maps using CAT12?
Volume-based atlases and ROI can be only applied to 3D data such as GM-maps and surface-based atlases are restricted to measures that are defined on the surface. These are completely different approaches that can't be compared directly.
The only way to compare volume and surface measures directly would be to map volume data to surfaces and to analyze both measures on the surface using a surface-based atlas. However, there are many ways to map measures from 3D (volume) space to surfaces and this will of course influence your results.
>
>3) I found the AAL atlas which is provided with CAT12. If I use this AAL atlas to extract ROI values from volume-based maps, which images (non-smoothed images [mwp1 & mwp2] or smoothed images [smwp1 & smwp2]) should I use?
I woud rather use unsmoothed images. However, you should keep in mind that the mwp1 images are modulated images where the measures are now in natives space because modulation controls for the volume changes that were made using the spatial normalization.
>Is there any way to extract the ROI values of the AAL atlas from surface-based maps?
No, see my answer above.
>Is it okay to directly apply FreeSurfer commands to the surf files (*.gii)?
This should work.
Best,
Christian
>
>
>Best regards,
>Wi Hoon
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