That is correct. MNI space IS NOT the correct place to measure areas, volumes, thicknesses.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Timothy Coalson <[email protected]<mailto:[email protected]>> Date: Wednesday, April 18, 2018 at 1:25 PM To: "Paul, Subhadip" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Estimation of surface area 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]<mailto:[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]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
