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@ -- 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 <http://about.me/matthewliptrot> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
