Understanding qsirecon scalarstats.tsv

Software Support
1

Summary of what happened:

I’m interested in extracting diffusion measures for specific tracts – specifically FA, MD, NODDI Vicm and ODI. When I ran QSIRecon, I used abcd_recon and I see that one of the outputs is sub-Subject1prelim_ses-1_acq-PA_run-001_space-ACPC_bundles-MSMTAutoTrack_scalarstats.tsv. Is this the right file I should be looking at? Would I extract the mean for each variable?

Also what is masked_mean, masked_median, etc. in this file?

Command used (and if a helper script was used, a link to the helper script or the command generated):

/opt/conda/envs/qsiprep/bin/qsirecon {root_dir}/QSI/preproc/qsiprep_output {root_dir}/QSI/recon/qsirecon_output participant --participant-label Subject1prelim --fs-license-file /opt/freesurfer/license.txt --recon-spec abcd_recon --nthreads 8 --omp-nthreads 8 --notrack -w {root_dir}/QSI/recon/qsirecon_work -v -v

Version:

1.2.1.dev0+g339140bfe.d20260218

Environment (Docker, Singularity / Apptainer, custom installation)

Apptainer

Screenshots / relevant information:

2

Hi @scchung,

Yes. One of those will be in each recon output folder and contain the bundle summary stats for each scalar made by that recon workflow.

Masked variables exclude voxels that are outside the brain mask, so in a sense it will clip the streamlines.

Whether you use mean or median is up to you, but I would caution that some metrics (especially RTOP) is prone to tiny (in size) but large (in magnitude) outliers that can skew means.

Best,
Steven