Connectivity matrix calculation

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Mattia De Francisci

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Aug 30, 2022, 10:49:29 AMAug 30
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Dear Frank,

I used DSI studio to obtain connectivity matrices starting from whole brain tractographies stored in .trk formats. I did the same using MRtrix (after converting my tractographies from .trk to .tck with https://github.com/nipy/nibabel/blob/master/nibabel/cmdline/trk2tck.py). I compared the mean matrices I obtained by using the two tools (from the same pool of subjects), and , although the general structure is preserved, DSI studio version of the mean structural connectivity matrix is sparser. I was wondering whether some filtering is applied in the connectivity matrix calculation in DSI (apart from the connectivity threshold, which I manually set to 0).

Best regards,
Mattia

Fang-Cheng Yeh

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Aug 30, 2022, 11:19:22 AMAug 30
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Yes, there is a threshold used to assign zero to the matrix entries if
their values are lower than a ratio multiplied by the maximum value of
the matrix. Usually, this ratio is 0.001 and can be adjusted at GUI or
command line (e.g. --connectivity_threshold).
Frank
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Mattia De Francisci

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Aug 31, 2022, 11:07:29 AMAug 31
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Dear Frank,
Thank you for your reply. I'm aware of that threshold and in fact I set it to 0, so that no entry would be artificially put to 0.

But I still get different results from MRtrix and DSI-studio. It seems like the number of connections reported in DSI matrix is systematically lower than the MRtrix version. So i was wondering if this could be explained somehow by the algorithm DSI studio uses to assign the streamlines to the node. Which is the condition for assigning a streamline endpoint to a node of the parcellatiion? Is there any constraint, maybe based on some anatomical assumption?

Thank you a lot,
Mattia

Fang-Cheng Yeh

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Sep 1, 2022, 10:41:27 PMSep 1
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Hi Mattia,

I don't recall anything special in calculating the matrix. It is
just a simple match of the rounded coordinates.

Perhaps we can run a simplified example (e.g. left arcuate
fasciculus) and see what may have caused the difference?

Best regards,
Frank

On Wed, Aug 31, 2022 at 11:07 AM Mattia De Francisci
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Mattia De Francisci

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Sep 9, 2022, 7:53:10 AMSep 9
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Hi Frank,

I think that MRtrix uses a radial search for assigning the streamlines to the nodes. I tried to change this rule and simply match the coordinates: now the matrices are much more similar. Thanks a lot!
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