External Email - Use Caution Dear FreeSurfer Developers,
I am trying to analyze functional connectivity using Freesurfer. When I checked FSFAST tutorial, it says: Sample command: "mkanalysis-sess -analysis fsrest.surf.lh -surface self lh -fwhm 5 -notask -nuisreg vcsf.dat 1 -nuisreg wm.dat 1 -mcextreg -polyfit 5 -nskip 4 -fsd fsrest -TR 4.5 -per-run" -mcextreg means that only top 3 components (I checked it was first 3 columns of mcprextreg) are used out of total 6 components. And indeed there are only 3 motion regressors in X.mat file. Freesurfer uses AFNI program to get motion correction parameters and AFNI uses all 6 components. (https://secure-web.cisco.com/12TJnsSiUh4nUlS0evLlfL-8nA36tqM4rfztjSsg7-3om9_ecCtXvMBvPYqjf0sKuLiZQn8Kc4JVAk2siFc7R9b_03WI4ju9aoZaa3RGNddJ6rWZ77949c6bJObCxos0x--p6-WKy89GVF6NEuQO9XARbvrlbU6PLWE6fc8EKApLIwE4AGMBKvY8GTpm-48nuYCz_feKDKtqo16zRuvxsXg6N2ct9tZ20yPtnCKpIxjhGQCsa02IvnHKdk-8k7CQ1y_BIQqQHk0Qw8k9Rz7Ud2xDKE0T-4U98Ig-DPt_kvVbU8fAPplOTT4aQchdtENcKWfIFk8X9A8PX4HnK3pYsbg/https%3A%2F%2Fafni.nimh.nih.gov%2Fpub%2Fdist%2Fedu%2Flatest%2Fafni_handouts%2Fafni05_regression.pdf) Do you have any reasons for having 3 as default? Kind Regards, Andy Junghyun Kim
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