 |
 |
Hi there, This post is in reference to "FA & MD value extraction within thalamus" (Wed, 9 Feb 2011). I would like to quantify FA (from TBSS) and grey matter volume (from FSL-VBM) in the 7 subregions of the thalamus, as determined by the Oxford thalamic connectivity atlas, in each of 90 subjects. To this end, I've tried to move the thalamic atlas into each subject's space. This is what I have done so far: 1. Moved the masked T1 image into MNI space flirt -in T1_masked -ref MNI -omat T1_to_MNI -out T1_masked_MNI 2. Inverted the resultant transformation matrix convert_xfm -omat MNI_to_T1 -inverse T1_to_MNI 3. Moved the thalamic atlas into T1 space flirt -in atlas -ref T1_masked applyxfm -init MNI_to_T1 -out atlas_T1 As you have probably expected, step 3 gave rise to labels "mixing up." What is the best way to solve this problem? That is, what is the best way to move the thalamic atlas into each subject's space? Could I threshold the thalamic atlas to create 7 masks, one each for the 7 subregions of the thalamus, move each of these masks into a subject's space, and then add them together? I would sincerely appreciate guidance on this issue. Thank you! Michael