subject=sub-hc001
fsd=msit
fmriprep_path=$subject/func
fsfast_path=fsfast
fmp_stem=${subject}_task-${fsd}_bold

# smoothing
fwhm=4
tr=1.75

# make the fsfast hierarchy
mkdir $fsfast_path/$subject
echo $subject > $fsfast_path/$subject/subjectname
mkdir $fsfast_path/$subject/$fsd
mkdir $fsfast_path/$subject/$fsd/001
fsfast_path=$fsfast_path/$subject/$fsd/001
mkdir $fsfast_path/masks

# extract the global mean value
mri_binarize --i $fmriprep_path/${fmp_stem}_space-T1w_brainmask.nii.gz \
             --o $fsfast_path/masks/brain.e3.nii.gz --min 0.5 --zero-edges --erode 3
meanval --i $fmriprep_path/${fmp_stem}_space-T1w_brainmask.nii.gz \
        --m $fsfast_path/masks/brain.e3.nii.gz --o $fsfast_path/global.meanval.dat --avgwf $fsfast_path/global.waveform.dat

declare -a hemis=("l" "r")
for hemi in "${hemis[@]}"
do
   uphemi=$(echo $hemi| awk '{print toupper($0)}')

   # convert fsnative surface files
   mri_surf2surf --srcsubject $subject --trgsubject $subject \
                 --sval $fmriprep_path/${fmp_stem}_space-fsnative.${uphemi}.func.gii \
                 --tval $fsfast_path/fmcpr.sm${fwhm}.${subject}.${hemi}h.nii.gz \
                 --fwhm-trg $fwhm --hemi ${hemi}h
   mri_convert $fsfast_path/fmcpr.sm${fwhm}.${subject}.${hemi}h.nii.gz $fsfast_path/fmcpr.sm${fwhm}.${subject}.${hemi}h.nii.gz -tr $tr
   
   # convert fsaverage surface files
   mri_surf2surf --srcsubject fsaverage --trgsubject fsaverage \
                 --sval $fmriprep_path/${fmp_stem}_space-fsaverage.${uphemi}.func.gii \
                 --tval $fsfast_path/fmcpr.sm${fwhm}.fsaverage.${hemi}h.nii.gz \
                 --fwhm-trg $fwhm --hemi ${hemi}h
   mri_convert $fsfast_path/fmcpr.sm${fwhm}.fsaverage.${hemi}h.nii.gz $fsfast_path/fmcpr.sm${fwhm}.fsaverage.${hemi}h.nii.gz -tr $tr
   
done

# convert mni305 
mri_convert -at $SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm -tr $tr --fwhm $fwhm \
            $fmriprep_path/${fmp_stem}_space-T1w_preproc.nii.gz \
            $fsfast_path/fmcpr.sm${fwhm}.mni305.2mm.nii.gz 

# convert native volume
mri_convert -tr $tr --fwhm $fwhm $fmriprep_path/${fmp_stem}_space-T1w_preproc.nii.gz \
            $fsfast_path/fmcpr.sm${fwhm}.sub-hc001.nii.gz