There is a bug in that command in the current release (1.2.3). Try the "dev_latest" version matching your operating system here:
http://brainvis.wustl.edu/workbench/ You might also consider using -cifti-parcellate to get the average values within all subcortical structures at the same time. If you need that result as text, there is -cifti-convert -to-text. Tim On Tue, May 9, 2017 at 11:45 AM, Astafiev, Serguei <astaf...@wustl.edu> wrote: > Hello, > > I am trying to create ROI from FS parcellation and extract z-values from > it. Steps 1 and 2 works. Step 3 gives me error message (core dumped): > > wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii > 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti > 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii > > /usr/local/pkg/workbench1.2.3/bin_rh_linux64/wb_command: line 15: 32654 > Segmentation fault (core dumped) > "$directory"/../exe_rh_linux64/wb_command > "$@" > > Can somebody tell me what is wrong? > > > > ## 1} Convert subcortical MNI ROIs to CIFTI > > wb_command -cifti-create-label 14035rois_subcort.dlabel.nii -volume > Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz > > > > ## 2} Select ACCUMBENS_RIGHT and create ROI for it > > wb_command -cifti-label-to-roi 14035rois_subcort.dlabel.nii > 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii -name ACCUMBENS_RIGHT > > > > ## 3} Match ROI dimensions to z-stat dimensions > > wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii > 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti > 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii > > > > ## 4} Extract values from ROI > > wb_command ‐cifti‐stats 100307_zstat1.dtseries.nii ‐reduce MEAN ‐roi > 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii > > > > > > Best regards, > > Serguei Astafiev > > Department of Psychiatry > > Washington University School of Medicine > > Campus Box 8134, > > 660 S. Euclid Ave, St. Louis, MO 63110 > > Phone: (314) 286-2205 > > FAX: (314) 286-0091 > > E-mail: astaf...@wustl.edu > > > > 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. > > > > > ------------------------------ > > 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
