New subject: registering MRI structural data with MEG volume converted data

20 May 2014


      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