Connectivity Matrix Computation

[Steven Jay Granger]

Hi Frank, 

I hope this note finds you well. 

I am wondering if there is a way to export individual tract files that make up the edge weights in graph theory analysis. 

In other words, after whole brain tractrography is completed is there a way to add an option to the --action=ana call to export or select the streamlines from the whole brain trk file that  'end' in reach ROI from the atlas? 

I am hoping to visualize the individual node-to-node connectivities without running separate tractrography. 

I realize this way be a big ask, however, it may be beneficial to see where the streamlines connecting A and B from graph theory pass en-route. 

Thanks so much in advance for your time! 

Best,

Steve 

[Frank Yeh]

Yes, --connectivity_value=trk
Hope it works for you.

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[Steven Jay Granger]

Hi Frank, 

Thanks for this! So it looks like that saves the .tt.gz files when referencing dsi studio locally. 

For some reason I am not able to get the --connectivity_value=trk through the docker version of DSI Studio. 

Example call here: 

/usr/local/bin/docker run --rm -v /Users/TestData:/data -v /Users/TestData:/output dsistudio/dsistudio:latest dsi_studio --action=ana --source=data/src_base.src.gz.icbm152.qsdr.1.25.R61.fib.gz --tract=data/count_connect.trk.gz --connectivity=opt/dsi-studio/dsi_studio_64/atlas/ICBM152/AAL2.nii.gz --connectivity_value=trk --connectivity_type=end 

This call runs and the terminal indicates the *tt.gz files are being saved however they do not appear in the TestData directory. 

Does a specific output need to be specified in order to get the --connectivity_value=trk command in docker to save the files? 

Thank you in advance for your time and for the help trouble shooting this problem. 

Best,

Steve 

[Frank Yeh]

The DSI Studio code that outputs the tracts does not specify any
directories. Thus DSI Studio will save tt.gz file in "pwd"
I am modifying the code to take --output=outputdirectory and will
release it shortly.
Frank

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