Those commands look correct, however MNI space may not be the correct place to make these measurements, as the registration distorts the subject anatomy to match a template (and the template happens to be significantly larger than the average subject). I suspect we do not actually recompute thickness in MNI space, so a thickness file in the MNINonLinear folder may simply be a copy from the T1w folder. Similarly, I would expect that our released values for surface area are measured in T1w space, which is a rigidly aligned, distortion corrected scanner space, matching the true shape of the subject's brain.
Note that with cifti files, you can use -cifti-parcellate to do these per-area summaries for all areas at once, rather than one at a time. You can use -cifti-convert -to-text to dump the data values after that (and -file-information will tell you the order of areas in the parcellated file). Tim On Wed, Apr 18, 2018 at 1:07 PM, Paul, Subhadip <[email protected]> wrote: > Dear HCP users, > > HCP has released thickness, surface area values based on DK > (Desikan-Killiany) atlas in a csv file. I would like to extract those > values using Destrieux atlas. To verify, whether am I following the correct > procedure, I have extracted regional cortical thickness data using MATLAB > from the HCP directory (/HCP_1200/100206/MNINonLinear/Native/) using DK > atlas and compared with HCP released values. The values are same. Now, I am > using connectome-workbench to estimate regional surface area using DK > atlas. However, the extracted value does not match with HCP provided value. > > To extract the area of left bankssts area (key 1) from > /HCP_1200/100206/MNINonLinear/Native/, I am using the following > connectome workbench commands: > > wb_command -gifti-label-to-roi 100206.L.aparc.native.label.gii > roi.func.gii -key 1 > > wb_command -metric-weighted-stats roi.func.gii -sum -area-surface > 100206.L.midthickness.native.surf.gii -show-map-name > > Could you please tell me whether am I using the correct commands? When I > used *pial*.surf.gii or *white*.surf.gii instead of *midthickness*.surf.gii > file in the second command, still the extracted value does not match with > the HCP released value. > > Once I figure out the correct approach, I would replace the > *aparc.*.label.gii file in the first command, with *aparc.a2009s*.label.gii > to extract surface area using Destrieux atlas. > > Thanking you, > > Subhadip > > > *Subhadip Paul* > > King's College London > > 16 De Crespigny Park, London > <https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF&entry=gmail&source=g>SE5 > 8AF > <https://maps.google.com/?q=16+De+Crespigny+Park,+London++SE5+8AF&entry=gmail&source=g> > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
