Dear all,
I was emailing today to ask a specific question about some of the specifics of 
mapping volumetric data to the surface with CIFTI files. I would like to use 
the HCP diffusion data to generate FA and MD maps using the DTIFIT command. 
Following this, I would like to map these to the surface (*IN NATIVE SPACE* 
importantly) so I can estimate mean values (FA/MD) over surface ROIs 
(potentially the freesurfer aparc in native space using the 
https://hcp-openaccess.s3.amazonaws.com/HCP_1200/996782/MNINonLinear/Native/996782.aparc.native.dlabel.nii).
 I have drafted a script below which will produce a surf.gii file containing 
the vertex-wise FA/MD values constrained to the GM cortical ribbon. I would 
then like to use something similar to the -wb_command –cifti-parcellate to 
produce a parcellated file with the mean FA/MD.

So briefly my questions are:

a)       Have I used the volume to surface mapping command correctly below with 
the correct surfaces?

b)       How do I go from a surf.gii file to a cifti file which is able to be 
parcellated?

Many Thanks
Dan


-----------------SCRIPT-------------
# A. Extract DTI data for each region

BASEDIR=XXXX
OUTDIR=XXXX #find output dir


for SUBJ in XXXX
do
cd  $BASEDIR/HCP_1200/$SUBJ/T1w/Diffusion/data.nii.gz

# 1. Select single b-val shell

select_dwi_vols \
data.nii.gz \
    bvals \
    dti_data \
    0 \
    -b 1000 \

# 2. Produce volume maps of both FA and MD

dtifit -k data.nii.gz -r bvecs -b bvals -m nodif_brain_mask.nii.gz \
    -o $OUTDIR/$SUBJ/dti --gradnonlin=grad_dev.nii.gz

# 3. Map these volumes (FA and MD) to surfaces to get good multimodal reg. Need 
to do twice
#              Once for each hemisphere

for hemi in L R
do
wb_command -volume-to-surface-mapping \
    - $OUTDIR/$SUBJ/dti/FA.nii \
    - 
$BASEDIR/HCP_1200/$SUBJ/MNINonLinear/Native/${SUBJ}.${hemi}.atlasroi.native.shape.gii
 \
    - $OUTDIR/$SUBJ/dti/FA.surface.shape.gii \
    -ribbon-constrained \
      
-$BASEDIR/HCP_1200/$SUBJ/MNINonLinear/Native/$SUBJ.${hemi}.white.native.surf.gii
 \
      
-$BASEDIR/HCP_1200/$SUBJ/MNINonLinear/Native/$SUBJ.${hemi}.pial.native.surf.gii
wb_command -volume-to-surface-mapping \
    - $OUTDIR/$SUBJ/dti/MD.nii \
    - 
$BASEDIR/HCP_1200/$SUBJ/MNINonLinear/Native/${SUBJ}.${hemi}.atlasroi.native.shape.gii
 \
    - $OUTDIR/$SUBJ/dti/FA.surface.shape.gii \
    -ribbon-constrained \
      
-$BASEDIR/HCP_1200/$SUBJ/MNINonLinear/Native/$SUBJ.${hemi}.white.native.surf.gii
 \
      
-$BASEDIR/HCP_1200/$SUBJ/MNINonLinear/Native/$SUBJ.${hemi}.pial.native.surf.gii
done
--------------------------------------


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