MRtrix3_connectome
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bids-apps
Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
There is no information (that I can easily see in Readme or help) about what are the files that are generated by the pipeline as output. Often, it is not...
For Siemens data (phase comes in in range [-4096, +4094]), converting to radians through applying scaling *only* (i.e. *not* applying an offset) is what is necessary to produce a complex...
Otherwise, the validity test can take a very long time (if the BIDS dataset has hundreds of subjects or more) If it's not supported downstream in the BIDS validator, maybe...
Branching discussion from #91, particularly from [this post](https://github.com/BIDS-Apps/MRtrix3_connectome/issues/91#issuecomment-734438245) onwards. Report of a FreeSurfer `recon-all` failure: ``` mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel freesurfer...
Hi Robert, I am using the version of MRtrix3_connectome from Dockerhub, having converted it to a Singularity container. I am running on our HPC. I guess I have never tried...
I was wondering if you had an example of the minimum BIDS inputs I would need to get going with the MRtrix3 connectome BIDSApp? Is there perhaps an example dataset?...
Some of the new parcellations in `dev` do not include cerebellar parcellation. Some also require a greater radial search distance due to incomplete GM coverage. Combining these two would mean...
Not in any particular order, just adding to (& subtracting from) the list as I think of them (/ implement them). - Lausanne multi-resolution - Yeo 7-network and 17-network parcellations...
Some of the new parcellations I am attempting to incorporate have unusual behaviour in terms of large gaps in between parcels. There's a few different ways this could potentially be...
Awaiting *MRtrix3* release and updating of this tool to the new Python API. New script `dwicat` could be used when concatenating across independent DWI series in order to approximate changes...