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Good morning, I am trying to reconstruct the tracts that were poorly reconstructed by tracula by editing control points of each tract (I already tried setting reinit=1 but it didn't work). This process is described in this article https://secure-web.cisco.com/10TqvkUm9LODp9Pl7m0fdHfu6lBQw4pYr1HxabnRgrdPw6DJlLfEJt0DensUI7pIy_ISvVwary2FwfNiKxSb-PMeR9m_okcY8jdtwlzC2ZoxXGuYv5EDf1s6L7BZJ8haDKByzBblNFHYu5wO4MbjJ1dwZiKp9vPyDO53jLUFhnhYvjQGBjBrDu4oNVtbTLEjzTS4NXCHsd5tqVWyTCJhpnaJPWNlP2cCoS1C3LH4IU7nydQyZbl_quHtx1le-_FS5Y6BthfQ6HPHZI6QKVRQ0jw7W_RU2aPz79g-9Xdyq-QSAwmXvZB3Id0iusmjbTfrBkNhx_6XxJrfhdc-lTq6D-w/https%3A%2F%2Fpmc.ncbi.nlm.nih.gov%2Farticles%2FPMC8006796%2F. In step 6 of section 'Data Processing and Quality Control' of that mentioned article, the authors say: "we converted the coordinates of the control points (https://secure-web.cisco.com/1OuJo9rzEYM7J_5SylW2YYQuH6HrdRZMFJLFYsT1uI6-2lJ...) from voxel space to Right-Anterior-Superior (RAS, anatomical coordinates) in order to view and edit in FreeSurfer’s freeview toolbox." I am confused about which transformation I have to do (from the ones mentioned in the link of step 6). Currently, without any transformation made, I see the control points (dlabel/syn/acomm_avg16_syn_bbr_cpts_7.txt) for the anterior commissure as in the figure attached in this email. As you can see, the points don't seem to be in diffusion space (but rather in the template space, MNI305). I am assuming that the transformation mentioned in the article sets the points in the position where the anterior commissure is supposed to be (and then the idea would be to edit them, save them and run trac-all -path -c for this tract). So my question here is: which transformation is it? I am inclined to believe it is the 4th mentioned in the link https://secure-web.cisco.com/1OuJo9rzEYM7J_5SylW2YYQuH6HrdRZMFJLFYsT1uI6-2lJ9NxcPbAjs1rxw4P0xxaNWA1rm-1W27amoiV9MiIoQREy7GS8aVZwlIwxR0xI76-G_xM16r0z4es9tr4CnjqfVjffsgdZOIwWGK-Ehp3sgOHLHhuo6MVqzkHsn-ouW0Yjw_pfLCjW5zXGmoJdOA0SPwNUuFq-5-HxmARpkoFaKTYaAbdnddC7qU9yNBqVEof16DINgsd0v3y89nPGr7o8yH243VK0GcavlpTwt9ECPnutFIZYWtAvVhW9yKmhddlPswMtbm_Q242sds5OjJYlVwJFIztZB5yw3Yj81nsQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems.
If you believe I am on the wrong track and there's abettert alternative, please let me know.
Warm regards, Mariana [image: imagen.png]
