Hi, HCP experts
I have a question regarding transferring HCP border ROI file for surface-based
tractography in FSL. What I did were (1) draw a border roi; (2) transfer the
border ROI to a metric file; (3) transfer the metric file to a label file; (4)
transfer the label file to a surface file for tractography. I used the
following steps:
============================================
echo "Step1: change borders to metric files..."
/usr/local/workbench/bin_rh_linux64/wb_command -border-to-rois
${targ_w_surface} ${datapath}/${1}/T1w/ROIs/${border}.border
${datapath}/${1}/T1w/ROIs/${border}.func.nii
echo "Step2: change metric to label files..."
/usr/local/workbench/bin_rh_linux64/wb_command -metric-label-import
${datapath}/${1}/T1w/ROIs/${border}.func.nii ''
${datapath}/${1}/T1w/ROIs/${border}.label.gii
echo "Step3: change label to surface files..."
echo "${datapath}/${1}/T1w/ROIs/${border}.label.gii" >
${datapath}/${1}/T1w/ROIs/labellist.txt
label2surf -s ${targ_w_surface} -o
${datapath}/${1}/T1w/ROIs/${border}.label.asc -l
${datapath}/${1}/T1w/ROIs/labellist.txt
================================
When I checked the generated surface ROI using the command "surf2volume" in FSL
by transforming it to a volume file, I find that my ROI turned to the *whole*
white matter surface, instead of only occupying the ROI. I have successfully
transformed label files generated via FreeSurfer to a surface file using the
command 'label2surf' and checked the results using the command "surf2volume".
They look reasonable (i.e., the results only occupy the ROI).
I also checked the metric, label files in WB and they all look reasonable
(i.e., having value of 'Label_1' and '1' in the label and metric files).
So, I wonder whether other users had similar issues and would appreciate any
information to fix the problem.
Many thanks!
Longchuan
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