Hi Donna,
Thanks for the info – I keep learning new functionality in wb_command! :-)
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?
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]<mailto:[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]<mailto:[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]<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:
• 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
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--
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
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