Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Glasser, Matthew
It should work if you skip the last step and use the dlabel file. Peace, Matt. From: Xavier Guell Paradis > Date: Wednesday, August 9, 2017 at 9:43 AM To: Timothy Coalson >, Matt Glasser

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Timothy Coalson
You need to have a dtseries (or dconn) file open before you can see any kind of connectivity. If you only have the labels/rois open, how do you expect it to figure out connectivity information? Note that we only have options for averaging things inside a label, the ROI file will not be useful in

Re: [HCP-Users] [SPAM] Brodmann area maps

2017-08-09 Thread Glasser, Matthew
Indeed the conversion from FreeSurfer annot format to GIFTI label format using FreeSurfer’s mris_convert does not preserve the probabilities (instead coloring every vertex with non-zero probability as a label). Really though, FreeSurfer only provides those labels on individual subjects as a

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
Dear Matt, Thank you for your reply. I have realized that a very curious thing happens: - If I open the dlabel file and right-click the cluster in wb_view, I do not see any option - If I open the dscalar file and right-click the cluster in wb_view, I do not see any option - If I open the dlabel

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
Dear Tim, Thank you for your reply I have made sure that I have the group .dconn file opened, and I can see that it is correctly opened because I can see connectivity when I click on any structure. However, I still have the same problem: I do not see the option of "Show Cifti Connectivity" when

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Timothy Coalson
If your "mycluster.nii" is in a different volume space than 222 MNI RPI space, then it may not let you use it that way. Compare the nifti header against this file in the HCP pipelines, using fslhd or wb_command -nifti-information -print-header: global/templates/MNI152_T1_2mm.nii.gz If it is

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
Dear Tim and Matt, Thank you very much for your reply. I tried -volume-label-import, followed by -cifti-create-label, followed by -cifti-all-labels-to-rois. After this, when I right-click the cluster in wb_view, I see the option "Show Data/Time Series Graph For Parcel [my cluster]" but I do not