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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