See inlline replies below.
On Aug 31, 2015, at 6:37 AM, Matthew George Liptrot <[email protected]> wrote: > Hi Donna, > > Thanks for the info – I keep learning new functionality in wb_command! :-) Me, too! Handy tool it is, and it keeps getting handier... > However, when I run that on the CIFTI connectivity file I don’t get such > results (see below). > Are there some hidden switches to get such an output? Or maybe those metrics > are only given for functional data? Sorry, you're right: I was using it on functional data stats. My bad. I like Tim Coalson's suggestion: wb_command -cifti-reduce matthew.dconn.nii MEAN matthew_mean.dscalar.nii wb_command -file-information matthew_mean.dscalar.nii The second command's output should give you a Inf/NaN column. Check the -cifti-merge-dense inputs for NaNs the same way. It sounded to me like you already checked the upstream inputs for NaN's, but using wb_command this way to reduce the dconn file to a summary stat for the purpose of making it easy to see how many NaN's there are in the file gives you a second opinion on the inputs' NaN status. > FYI, I’m using wb_command v1.1.1 on Linux. > > Cheers, > > M@ > > $ wb_command -file-information Conn3.dconn.nii > Name: Conn3.dconn.nii > Type: Connectivity - Dense > Structure: CortexLeft CortexRight > Data Size: 33.33 Gigabytes > Maps to Surface: true > Maps to Volume: true > Maps with LabelTable: false > Maps with Palette: true > All Map Palettes Equal: true > Map Interval Units: NIFTI_UNITS_UNKNOWN > Number of Rows: 91282 > Number of Columns: 91282 > Volume Dim[0]: 91 > Volume Dim[1]: 109 > Volume Dim[2]: 91 > Palette Type: File (One for all maps) > CIFTI Dim[0]: 91282 > CIFTI Dim[1]: 91282 > ALONG_ROW map type: BRAIN_MODELS > Has Volume Data: true > Volume Dims: 91,109,91 > Volume Space: -2,0,0,90;0,2,0,-126;0,0,2,-72 > CortexLeft: 29696 out of 32492 vertices > CortexRight: 29716 out of 32492 vertices > AccumbensLeft: 135 voxels > AccumbensRight: 140 voxels > AmygdalaLeft: 315 voxels > AmygdalaRight: 332 voxels > BrainStem: 3472 voxels > CaudateLeft: 728 voxels > CaudateRight: 755 voxels > CerebellumLeft: 8709 voxels > CerebellumRight: 9144 voxels > DiencephalonVentralLeft: 706 voxels > DiencephalonVentralRight: 712 voxels > HippocampusLeft: 764 voxels > HippocampusRight: 795 voxels > PallidumLeft: 297 voxels > PallidumRight: 260 voxels > PutamenLeft: 1060 voxels > PutamenRight: 1010 voxels > ThalamusLeft: 1288 voxels > ThalamusRight: 1248 voxels > ALONG_COLUMN map type: BRAIN_MODELS > Has Volume Data: true > Volume Dims: 91,109,91 > Volume Space: -2,0,0,90;0,2,0,-126;0,0,2,-72 > CortexLeft: 29696 out of 32492 vertices > CortexRight: 29716 out of 32492 vertices > AccumbensLeft: 135 voxels > AccumbensRight: 140 voxels > AmygdalaLeft: 315 voxels > AmygdalaRight: 332 voxels > BrainStem: 3472 voxels > CaudateLeft: 728 voxels > CaudateRight: 755 voxels > CerebellumLeft: 8709 voxels > CerebellumRight: 9144 voxels > DiencephalonVentralLeft: 706 voxels > DiencephalonVentralRight: 712 voxels > HippocampusLeft: 764 voxels > HippocampusRight: 795 voxels > PallidumLeft: 297 voxels > PallidumRight: 260 voxels > PutamenLeft: 1060 voxels > PutamenRight: 1010 voxels > ThalamusLeft: 1288 voxels > ThalamusRight: 1248 voxels > > > > > On 25/8/15 15:48 , "Donna Dierker" <[email protected]> wrote: > > wb_command -file-information gives you stats like this: > > Map Minimum Maximum Mean Sample Dev % Positive %Negative > Inf/NaN Map Name > > > On 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: > • Generate 3 separate targets (left surface, right surface, subcortical > voxels) > • 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). > • The multiple probtrackx2 runs are combined with FSL’s fdt_matrix_merge. > This gives us 3 FSL .dot files. > • Convert each of the three .dot files to .dconn using <wb_command > -probtrackx-dot-convert> > • 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 > 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 > > > > > > > -- > Matthew George Liptrot > > 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
