Hello Freesurfer Experts,

We've used the following tcsh script to convert MEG surface data, morphed to fsaverage .w paint (every timestep) format, to volume data in NIFTI format:

#  Convert to .nii format (volume from surface data of dSPM) placing .nii files in NII_DIR
# FREESURFER_HOME is the base directory for FreeSurfer; sourcing from SetUpFreesurfer.sh
setenv FREESURFER_HOME /apps/freesurfer/ && source ${FREESURFER_HOME}SetUpFreeSurfer.csh
# set file numbers denoting each time step
set Tmin = -0200 && set Tstep = 10 && set Tmax = 1000
#
foreach FileNum (` seq -w $Tmin $Tstep $Tmax ` )
    # CONVERT SURFACE DATA TO VOLUME DATA FROM PAINT TO MGZ to NII
    mri_surf2vol --surfval ${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.w paint --hemi lh --volreg ${SUBJECTS_DIR}/fsaverage/mri/transforms/reg.mni152.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/T1.mgz  --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.mgz
    mri_convert ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.mgz ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.nii
    mri_surf2vol --surfval ${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.w paint --hemi rh --volreg ${SUBJECTS_DIR}/fsaverage/mri/transforms/reg.mni152.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/T1.mgz  --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.mgz
    mri_convert ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.mgz ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.nii
    # mri_concat does temporal concatenation.  Done this way, each image will include the left
    # hemisphere solution, and then the right hemisphere solution.  You have to do this separately
    #for each hemisphere, and then add the two hemispheres together using something like
    #fslmaths or 3dcalc.
    # Have to convert mgz to nii first using e.g.: mri_convert input.mgz output.nii
    # e.g., 3dcalc -a left.nii -b right.nii -expr 'a+b' -prefix test_combined.nii
    
    # MERGING OF HEMISPHERES (.nii) AT EACH TIMESTEP
    ${AFNI_DIR}/3dcalc -a ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.nii -b ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.nii -expr 'a+b' -prefix ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0.nii

set ExecString = 'mri_concat '
foreach FileNum (` seq -w $Tmin $Tstep $Tmax ` )
    set ExecString = "${ExecString} ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0.nii  "
end

The .nii files come out uniform size and a colleague suggested that I add a baseline to the original data. It seems like the issue is happening at the mri_convert step and the T1.mgz fsaverage template seems to not register properly. Is there some syntax I should be adding to the --template option in mri_surf2vol? Perhaps it's something else.

-Franklin