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PennLINC / qsiprep

Preprocessing of diffusion MRI
http://qsiprep.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Question about connectivity matrix #376

Closed sreekarchigurupati closed 2 years ago

sreekarchigurupati commented 2 years ago

Hello, This is my first time running qsiprep. I am trying to run mrtrix_singleshell_ss3t_noACT on a single subject. I want to generate a connectivity matrix out of this. The command generates a file named sub-10506_space-T1w_desc-preproc_dhollanderconnectome.mat inside the folder out/qsirecon/dwi. Is this the connectivity matrix? If not, how do we get it? This is not visualized in the HTML report. Is there anyway to include this in the report?

Command Used: qsiprep-singularity ~/data ~/out --output-resolution 1.2 --fs-license-file ~/license.txt -w ~/data/working --use-syn-sdc --force-syn --denoise-method patch2self --unringing-method mrdegibbs --no-b0-harmonization --nthreads 60 --recon_spec mrtrix_singleshell_ss3t_noACT

Thanks Sreekar

sreekarchigurupati commented 2 years ago

qsiprep version used: v0.15.3

pcamach2 commented 2 years ago

Hi @sreekarchigurupati,

The .mat file is a MATLAB file that should contain the NxN connectivity matrices for the parcellations and edge-weighting schemes associated with the mrtrix_singleshell_ss3t_noACT workflow. You can open them in MATLAB or use a package for your programming language of choice (e.g. scipy.io for python).

Cheers, Paul

sreekarchigurupati commented 2 years ago

Thank you