# Empty nodes in connectome

**URL:** <https://community.mrtrix.org/t/empty-nodes-in-connectome/8880>\
**Category:** Uncategorized\
**Tags:** connectomics, tractography\
**Created:** [November 4, 2026, 2:11pm UTC](https://community.mrtrix.org/t/empty-nodes-in-connectome/8880 "2026-11-04T14:11:25Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Beatrice\_Bravi](https://community.mrtrix.org/user_avatar/community.mrtrix.org/beatrice_bravi/32/4768_2.png) [@Beatrice\_Bravi](https://community.mrtrix.org/u/Beatrice_Bravi)\
**Post date:** [November 4, 2026, 2:11pm UTC](https://community.mrtrix.org/t/empty-nodes-in-connectome/8880/1 "2026-11-04T14:11:25Z")

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Dear experts,

I’m using the TractoPrep container [TractoPrep Processing Manual — TractoPrep v1.0.6 documentation](https://tractoprep.readthedocs.io/en/latest/) to obtain connectome from my DWI data.

It leads from preprocessing to the final connectome across different steps, mostly automatically (using several mrtrix and fsl commands).

I have different DWI acquisitions, single- and multi-shell, but the container seems to handle both of them.

However, for a considerable proportion of subjects acquired with a specific sequence, the final connectome presents a lot of empty nodes (totally disconnected ROIs). This specific acquisition is single-shell and includes 35 directions and b=900. Here attach an example of the QC after the tracto step (which basically works with **`dwi2fod, tckgen and tcksift`** ).

 ![image](https://community.mrtrix.org/uploads/default/original/2X/b/b8b5b2c8be06977a526cd52edcc5ad04707a6786.jpeg)

My first question is: what could be the problem that creates several disconnected nodes?

And then: what is a kind of cutoff to decide whether to use or exclude a connectome for analyses (in general, also when working with the standard mrtrix pipeline)?

Last: is it really appropriate to also use single-shell data to build a connectome?

Thank you so much in advance for any help!

Best,

Beatrice