Steven Meisler

I mounted my local version of `fsr-checkxopts` (from FS6) to the container and it appears to be progressing.

This may be because, in a similar fashion, `getfullpath` is not in the docker container, but may be called by FreeSurfer.

Not directly answering your question, but if you have multishell data, why not use the multi-shell multi-tissue (MSMT) pipeline? While typical DTI tensors tend to get wonky at high b-vals...

Hmmm, the command is being generated and executed without error, but only the un-sifted tractogram is ultimately output, and under the sift name. I think I confused output_node vs ds_tck_file,...

1) Yes, for qsirecon to run , `--recon-spec` must be specified 2) That error doesn't actually seem to be a problem, since it comes after the last step of preprocessing...

I tried changing the `mapping_definition` to `None`, but I am still left with a very sparse tractogram (Original 10M streamlines, `tcksift` to 2.5M streamlines, AFQ version has 3900 streamlines). As...

Below. No apparent errors. ``` WARNING:py.warnings:The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes...

The data for one subject may be found here: https://drive.google.com/drive/folders/1j6QUBaO2lAYNUhSsWLzlYyUAB8aCLIDF?usp=sharing For the result I described in my last message, I was sure that I input the HCP preprocessed DWI image,...

Thanks, I appreciate the update!

To clarify, this is more of a PyAFQ issue than it is QSIPrep, but I have had this issue of sparse tractograms and segmentations with both QSIPrep processed data (google...