I don't suppose you're seeing NaNs specifically in matlab after using ft_read_cifti? I don't know of anything else that is expected to add NaNs.
Could you do "wb_command -cifti-reduce <your dconn> MEAN mean.dscalar.nii" and then do -file-information on that? If that shows NaNs, I suggest also running it on the inputs to -cifti-merge-dense to check for NaNs there. Tim On Tue, Aug 25, 2015 at 6:32 AM, Matthew George Liptrot < [email protected]> wrote: > 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]> 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]> > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
