Dear experts,
I'm trying to obtain a NxN connectivity matrix (N regions from atlas2009) with
data (preprocess) from HumanConnectumProject with probtrackx2. I want to have a
surface as seed.
I follow the pipeline below but I obtain results which doesn't seem correct :
some pixel of the seed surface are not connected to any region.
First, I use the annotation2label to obtain labels :
mri_annotation2label --subject 105115 \
--hemi lh \
--annotation $FREESURFER_RESULT_DIR/label/lh.aparc.a2009s.annot \
--outdir $FREESURFER_RESULT_DIR/labels \
--surface white
mri_annotation2label --subject 105115\
--hemi rh \
--annotation $FREESURFER_RESULT_DIR/label/rh.aparc.a2009s.annot \
--outdir $FREESURFER_RESULT_DIR/labels \
--surface white
Then, I generate seeds volume from labels and I copy all path to seeds volume
in a text file.
Here the script :
for hemi in {lh,rh}
do
for lab in `cat $FREESURFER_RESULT_DIR/label_order.txt`
do
label=$FREESURFER_RESULT_DIR/labels/$hemi.$lab.label
vol=${label/%.label/.nii.gz}
mri_label2vol --label $label --temp
$FREESURFER_RESULT_DIR/anat/orig.nii.gz --o $vol --identity --fillthresh 0.5
echo $vol >> $FREESURFER_RESULT_DIR/seeds.txt
done
done
To obtain the waypoints, I use:
mri_binarize --i $FREESURFER_RESULT_DIR/mri/aparc+aseg.mgz --match 2 --o
$FREESURFER_RESULT_DIR/anat/wm.{r,l}h.nii.gz
And I copy both wm.{r,l}h.nii.gz in a text file waypoints.txt.
To obtain ventricles.nii.gz, I use :
mri_binarize --i $FREESURFER_RESULT_DIR/mri/aparc+aseg.mgz --ventricles --o
$FREESURFER_RESULT_DIR/anat/ventricles.nii.gz
Finally, I use probtrackx2 like that,
probtrackx2 -V 2 \
-x \
/Human/HumanConnectome/10unrelatedSubjects_preproc/105115_probtrackx/Structural_preproc/T1w/fsaverage_LR32k/105115.R.white.32k_fs_LR.surf.gii
\
-l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000
--fibthresh=0.01 –distthresh=0.0 \
--sampvox=0.0 –omatrix1 \
--stop=$FREESURFER_RESULT_DIR/seeds.txt \
--forcedir --opd \
-s $BEDPOSTX_RESULT_DIR/merged\
-m $DIFFUSION_DIR/nodif_brain_mask\
--waypoints=$FREESURFER_RESULT_DIR/waypoints.txt \
--waycond='AND' \
–dir=matrix_surf_rh_to_Nvolume \
--avoid=$FREESURFER_RESULT_DIR/anat/ventricles.nii.gz
So I have few questions :
First, can you confirm me that all data preprocess from HCP are in the same
space : Diffusion / Structural_preproc / Structural_preproc_extented ?
Then, Am I doing something wrong in my pipeline ?
Someone has already succeed to obtain a NxN connectivity matrix with this tools
and data from HCP ?
Thank you for your help,
Best regards,
Danaele
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