araikes

Tagging into this as I'm running into the same issue and want to keep track of progress on this.

Looks like a CFA file is already being generated and just not used.

After a bit of checking, it appears that the plotting functions cannot make necessary writes to an X11 folder. The following works (though there are a couple of warnings about...

Alright.. Figured it out the issue but don't know how to fix it. The acquisition was a multi-echo T2 RARE so I have: ``` ##$VisuAcqEchoTime=( 6 ) 7 21 35...

I tried setting modality to "MESE" in the dicominfo.csv manually but it still failed.

1. `brkraw bids_helper dicoms/ nifti/.brkraw/dicominfo -j` 2. Manually edit the CSV to clean up animal names and set the "dir" parameter for the DWI data (LR/RL). Resave as `dicominfo_final.csv` 3....

@gdevenyi, I now have the same problem converting a dataset with no multiecho data. This would suggest that the JSON parser differs between `tonii -b` and `bids_convert`. I've been trying...

I'll try that, but I found the general error. The error codes weren't sufficient to get to it, but it was actually the B0 Map that we acquired with the...

@dvm-shlee Multi-echo images should be individual echo images with the appropriate suffix (e.g., MESE or MEGRE). See https://bids-specification.readthedocs.io/en/stable/appendices/file-collections.html

I want to get back to this but haven't had a chance to yet. There are some issues with OS version and dependencies for MRtrix `3.0.3` and `3.0.4` but I...