Hello freesurfer experts,
I am trying to register a functional volumetric image (.nii) into a surface (.gii) to produce a functional surface image (.gii), where each node of the image will contain a time-series. My purpose for doing this is to use freeview to visualize the time-series of each node. I've tried to do this using bbregister to obtain a registration matrix of the functional image into a structural image, mri_vol2surf to resample the functional volume, and finally mris_convert to convert the resampled functional volume into a (4d) functional surface. The details of how I used these commands are as follow:
bbregister --s AL_subject/AL \
--mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii \
--reg /home/osboxes/Desktop/AL_registrations/AL.mat \
--init-fsl --t2
mri_vol2surf --mov /home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet. feat/filtered_func_data.nii --reg /home/osboxes/Desktop/AL_registrations/AL.mat --projfrac 0.5 --hemi lh --o /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh --projfrac 0.5 --interp nearest
mris_convert -f /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh \
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/EEG_fMRI_FreeSurfer _anatomies/AL_subject/AL/surf/lh.white \
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii
Although these commands run without any error, the result (AL_surface_time_series_lh.gii) cannot be opened in freeview, presumably because the produced 4d functional surface does not have the necessary surface information (vertices, faces) needed by freeview in order to open it. More specifically, when I try to open it I get MRISread failed
mriseadGIFTIfile: mris is NULL! found when parsing file /home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii in the terminal.
I am new user of freesurfer and I would appreciate if someone could help me with this.
Thanks, Prokopis