I am exploring the connectivity maps generated by the QSIRecon. For this I make use of the sub-OAS30003_ses-d3731_space-ACPC_connectivity.mat file stored in the derivatives…/…/…/dwi directory and load in Matlab for visualization. Now, I am searching for the possible tck2connectome command used in this process if this is used.
Can you please point me to the command and it’s location used for this purpose?
Q1. a) We have Thalamic nuclei labels segmented using THOMAS segmentation technique using native space T1w images. Why is that we need to warp these labels to MNI space for compatibility with QSIRecon?
b) Can we still use the native space segmentation labels for generating the connectivity maps?
c) Also, fiber tracts generated by the QSIRecon we believe are in AC-PC space?
Q2. Where does the AC-PC to MNI warps located in the QSIPrep or QSIRecon output directories?
QSIRecon uses the MNI-to-subject warp to put atlases into subject space.
QSIRecon is built around standard space atlases. Although, I suppose it is possible to make an MNI version of each subject’s segmentation, and make each one a “separate” atlas. At that point though, you might just be better off running tck2connectome separately from QSIRecon.