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Hello FreeSurfer Developers,
I'm attempting to acquire the hippocampal subfields and nuclei of the amygdala using a high resolution of 0.333 mm3. However, when comparing the results of using the Freesurfer Coordinate System in matlab, using the reported tkrRAS to VoxCRS equation, and the results of Freeview, by manually inputting the tkrRAS, they report different subfields. We were wondering whether this the matlab coordinate system is getting rid of information or the freeview is adding information? How could get more precise information with the matlab coordinate system?
When looking closely, it appears that VoxCRS coordinates can have multiple subfields within the same integer by slightly altering the tkrRAS coordinates and noticing the subfield region name change using freeview.
For example, we have a tkrRAS coordinate of [-24.65, -7.82, -21.04]. Putting this coordinate into freeview it gives us an "Unknown" region. Using the matlab coordinate system, we first transform the tkrRAS coordinates into the high resolution tkrRAS coordinates due to the mismatch of volume between the lower and high resolution. Then we use, VoxCRS = inv(Torig)*[tkrR tkrA tkrS 1]' to get the VoxCRS and then check the volume to get the subregion. It gives us a "CA1" region.
I have searched the archive of past problems. However, no similar problems have reported.
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-V6.0.02beb96c Freeview Version: Version 2.0 Build Jan 18 2017 16:48:55 MATLAB Version: R2018b Ubuntu Version: 18.04.4
Freesurfer Coordinate System link: https://secure-web.cisco.com/1a-L_exiDRUdrPGFnZvtMx-VhHRhWEfIDjmkx_H9zNuPhjN...https://secure-web.cisco.com/1a-L_exiDRUdrPGFnZvtMx-VhHRhWEfIDjmkx_H9zNuPhjNrW8-tM1p4TUNbGRGfizhMmwSjWBLEhcdLmgpDgawRXhV7qtbzzJlREUFhManFIzXldzLBP5j3wnPCsIqwcKJWBTut3td_uLvK4_hwFFcBQj75nCLngPFDm4uScJZCfvbgGCW4i_yC-UPpXwbk9jI_rb6Dy5Q8uG2mb-4tR_mVHNb9YkqOTAmlWM8XgScjVrKRhulsljrK1rfRVihM5v_V08wZOUIKA9XYFAH6EaBbrVr5VHm4vPYjPuosM7WUaQcpoX0pRIcyQyFRA0c2Cgfrlf3t_nCS30Ml2MXFLIA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems Segmentation of hippocampal subfields and nuclei of the amygdala link: https://secure-web.cisco.com/1f_b9T_6PJ49eQDQwBXq2S2L2mj5oSdjOEWB7Fjc78JCCPE...
Sincerely, Jarod