Missing output with CLI QSDR reconstruction

[Hannah Lindsey]

I ran the following command on a bunch of data and noticed that the reconstructed datasets don't include AD, MD, or gFA, even though I included them in --other_output:

dsi_studio \

--action=rec \

--source=src/sub*.sz \

--method=7 \

--param0=1.25 \

--check_btable \

--qsdr_reso=2 \

--other_ouput=qa,rdi,iso,qir,gfa,fa,ad,md,rd \

--output=fib

When I select those metrics via GUI reconstruction, they are included in the reconstructed datasets.

I also noticed that the reconstructed data from the CLI versus the GUI, using the same options (except CLI datasets don't include MD, AD, gFA), produces slightly different metric values for the same tracts (average of ~.05 difference across QA, FA, RD, ISO, QIR, and RDI) and autotrack produces slightly different results with the same parameters.

I'm currently performing tractography on over 600 datasets reconstructed on the CLI. The tractography has taken about 10 hours so far and is only about halfway finished, so I'm wondering if I can re-reconstruct the datasets in the GUI, so I can also get AD, MD, gFA, but use the tracts I've already generated from the datasets reconstructed in the CLI. 

Given your knowledge of what might cause those slight differences in results and stats, do you think it will be necessary to re-run the tractography after I re-reconstruct the data with the additional output in the GUI?

Alternatively, is this something you can quickly fix in the code so I can get those other outputs by reconstructing on the CLI?

Thanks!

Hannah

[Frank Yeh]

--other_ou"t"put

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[Hannah Lindsey]

Omg… that’s embarrassing haha. Thanks for catching that!

_________________________________

Hannah M. Lindsey, PhD

Research Associate

TBI and Concussion Center

Department of Neurology

University of Utah

On Sep 15, 2025, at 3:47 pm, Frank Yeh <fran...@gmail.com> wrote:



[Frank Yeh]

Haha, no problem!