Hello Freesurfer Experts,
I have a question to ask about extracting the mean time series from resting-state fMRI (239 volumes).
I have used bbregister to bring the 4D fMRI data into T1 space. My next objective is to project the data onto the fsaverage surface, and then extract the mean time series for each ROI.
These are my steps so far. Can anyone let me know if I am on the right/wrong track?
bbregister --s $i --mov ${i}_medn.nii (fMRI resting-state) --init-fsl --t2 --reg ${i}/fmri/fmri_t1.dat --o ${i}/fmri/fmri_t1.mgz
mri_vol2surf --src ${i}/fmri/fmri_t1.mgz --out ${i}/surf/lh.fmri.mgh --hemi lh --projfrac 0.5 --interp nearest --regheader ${i} --trgsubject fsaverage
mri_segstats --i ${i}/surf/lh.fmri.mgh --annot fsaverage lh aparc --sum ${i}/stats/lh.fmri_aparc.sum
Ultimately, how may I derive a 239 (volumes) x 34 (ROIs per hemisphere) matrix of the data?
Appreciate your help. Thanks!
Best Wishes, Elijah
Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK