Hello everyone,
I'm currently running a combined TMS/fMRI experiment. Thus, as first step in my experiment, we ran the neuronavigation procedure on the participant structural scan to find the stimulation point based on anatomical landmarks. Then, before and after the TMS stimulation, we ran functional resting state fMRI.
As an output, I have the 3D coordinates for each participant based on the not preprocessed structural scan I use for the neuronavigation.
I have already run all the preprocessing steps for my functional data (slice-timing correction, realigning & unwarp with fieldmap data, coregistration, segmentation, and normalization). Now, I would like to run seed-based connectivity analysis from the stimulated point to the whole brain, but I cannot understand where to find the conversion matrix to transform the 3D coordinates from the native space to MNI.
I already tried to generate binary ROI masks in the native space (radius = 9) and then use the deformation field file ("y_...nii") to normalize the ROIs, but when I do so, my spherical ROIs became ovals, and I honestly don't know if this procedure it's correct.
After segmentation, I have the "..seg8.mat" file for each participant. Can anyone explain to me the details of the variables that are stored in this file? Is it here that I can find the deformation matrix that I need to transform my native coordinates?
I appreciate any help you can provide.
Enrica
|