Hi Alfonso, 

Several of the seed regions appear to be full Brodmann areas while others are described by specific coordinates. Can you clarify a rationale for this discrepancy? Is there anywhere within the program that will divulge more information regarding the seed regions used in the connectivity analyses (e.g. number of voxels)? Furthermore, can you explain how these choices (size of seeds: BA vs. coordinates) may impact the seed-to-voxel findings?

Thank you!

Maggie

Hi Margaret,

In release 14o we changed the default atlas from a Brodmann areas atlas to the current Harvard-Oxford atlas (the source of the BA.img atlas was http://www.talairach.org; it is described in conn/utils/otherrois/TDreadme.txt; the source of the Harvard-Oxford atlas is described in conn/rois/atlas.info). The coordinates that you refer to are probably the ones in the original default mode network files. These are also no longer part of the default ROIs; they were derived from Fox et al. published results, and their information is described in the file conn/utils/otherrois/dmn.info. Currently the DMN areas that are part of the default ROIs were obtained from a ICA analyses of 498 subjects from the Human Connectome Project (and this is described in conn/rois/networks.info). If you want to know the size/number of voxels within each ROI, you can for example use the following syntax:

  [sizes, names] = rex('./myROI.nii','./myROI.nii'', 'summary_measure','count', 'level','clusters');


which will return the size of each ROI in the "./myROI.nii atlas file in the "sizes" variable, and the ROI names in the "names" variable.
Hope this helps
Alfonso

Originally posted by Margaret O'Connell: