Hi Stam, Yep, workbench opens them fine. If I load in the dconn file, a surface and the greyordinates.dscalar file, then I can see the connectivity maps as I click different parts of the surface. Is there a better way to check if the values are reasonable? E.g. Would the histograms report if NaNs are present?
Good to hear about the FSL release! I guess though that this is a wb_command bug (or a bug in my use of it! :-) Cheers, M@ On 24/8/15 14:40 , "Stamatios Sotiropoulos" <[email protected]<mailto:[email protected]>> wrote: Hi Matthew No, they are not meant to be there. Can you open and display the dconn file in workbench? FYI, there will be a new FSL release sometime this or the next week. It will have some bug fixes in probtrackx2 and some new features. It may be the case that this problem disappears with the new version. Cheers Stam On 24 Aug 2015, at 08:24, Matthew George Liptrot <[email protected]<mailto:[email protected]>> wrote: Hi all, We’ve been using the HCP DWI data to generate dense connectomes in ‘matrix3’ format. Following previous advice, we are doing this in multiple stages: 1. Generate 3 separate targets (left surface, right surface, subcortical voxels) 2. For each, run probtrackx2 (seed = white matter voxels, target as above) multiple times using the ‘-rseed’ option (1000 streams per voxel as a robustness / computational trade-off). 3. The multiple probtrackx2 runs are combined with FSL’s fdt_matrix_merge. This gives us 3 FSL .dot files. 4. Convert each of the three .dot files to .dconn using <wb_command -probtrackx-dot-convert> 5. Merge the three .dconn files using <wb_command -cifti-merge-dense> to obtain the final 92K x 92K dconn matrix. The problem is that we get both NaN’s and zeros in the final, merged dconn matrix. Presumably we should not have any NaN’s, as the numbers should just represent count statistics? We looked into the outputs at different stages, and it seems that the NaN’s only appear after Step 5. So our question is: are the NaN’s meant to be there, and if so, what do they represent? If not, is this a bug or a mistake on our part? Many thanks for any help! M@ <http://about.me/matthewliptrot> -- Matthew George Liptrot <http://about.me/matthewliptrot> Department of Computer Science University of Copenhagen & Section for Cognitive Systems Department of Applied Mathematics and Computer Science Technical University of Denmark http://about.me/matthewliptrot _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
