Re: [HCP-Users] (no subject)

[Glasser, Matthew]

I just forwarded something that should answer this.  Apparently I’ve been giving some mis-information: FSL’s label2surf program doesn’t work with GIFTI, so one needs to use surf2surf .func.gii metric ROIs like this: surf2surf -i ${Subject}.${Hemisphere}.white.surf.gii -o <output probtrackx format ROI surface> --values=${Subject}.${Hemisphere}.roi.func.gii Peace, Matt. From: Longchuan Li <leonad...@yahoo.com> Reply-To: Longchuan Li <leonad...@yahoo.com> Date: Monday, July 14, 2014 at 3:02 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] (no subject) 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   _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users