Turn off network measures in --action=ana

[Maxwell Bertolero]

Would it be possible to have it be an option, or even the default, to not write out the network measures? I need to generate about 8000 connectivity matrices (running a searchlight type algorithm), so it would be great to call this function quickly, and only save out the connectivity.mat file.

Thanks!

[Fang-Cheng Yeh]

A new build is underway: https://github.com/frankyeh/DSI-Studio/actions/runs/3100528607

check out the --connectivity_output option at https://dsi-studio.labsolver.org/doc/cli_t3.html

On Wed, Sep 21, 2022 at 3:20 PM Maxwell Bertolero <mbert...@gmail.com> wrote:

Would it be possible to have it be an option, or even the default, to not write out the network measures? I need to generate about 8000 connectivity matrices (running a searchlight type algorithm), so it would be great to call this function quickly, and only save out the connectivity.mat file.

Thanks!

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[Max Bertolero]

Thanks!! 

Will that work for both action=trk and action=ana? 

I like action=ana, as I can precompute the tracts, then make the matrix from a bunch of different parcellations. 

Thanks again,

Max Bertolero, PhD
Neuroinformatics Software Architect
Nous Imaging 

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[Fang-Cheng Yeh]

It should be, because the post-tracking pipeline is identical.

I would suggest using --action=trk and skipping tractography saving/loading by --output=no_file.

Frank

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[Max Bertolero]

Ah, I thought I was saving time by running:

dsi_studio --action=trk --source={fib_file} --output={tract_output}

And then: 

dsi_studio --action=ana --source={fib_file} --tract={tract_output} --connectivity={connectivity} --connectivity_value=count --export=connectivity --output={output}
        

Are the tracts still recalculated in dsi_studio --action=ana if I pass a --tract?

Thanks so much,

Max Bertolero, PhD
Neuroinformatics Software Architect
Nous Imaging 

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[Fang-Cheng Yeh]

It would be much faster by 

dsi_studio --action=trk --source={fib_file} --output=no_file --connectivity={connectivity} --connectivity_value=count --export=connectivity --connectivity_output=matrix

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[Max Bertolero]

Sweet, thanks! 

Max Bertolero, PhD
Neuroinformatics Software Architect
Nous Imaging 

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[Fang-Cheng Yeh]

BTW, you don't need --export=connectivity

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[Max Bertolero]

This absolutely rips. Thanks so much Frank! 

Max Bertolero, PhD
Neuroinformatics Software Architect
Nous Imaging 

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