Locate or access or open mtrix_singleshell_ss3t_ACT-hsvs outputs after successful QSIprep run?

Software Support
1

Dear neurostars experts,

I am writing in the hopes that someone might be able to help me locate/access/open mrtrix_singleshell_ss3t_ACT-hsvs outputs!! :blush:

Summary of what happened:

I sincerely apologize if this is an elementary question or the answer was posted elsewhere (I saw this but am still a bit confused: Output of reconstruction workflow in Qsiprep seems incorrect - #6 by mattcieslak) but am hoping someone here might be able to help.
I successfully ran mrtrix_singleshell_ss3t_ACT-hsvs for one participant on an apptainer/singularity, and have looked through the /derivatives/ folder (especially /derivatives/qsirecon/), but can’t figure out what outputs to look for and what to do with them. I assumed I’d find some sort of .csv spreadsheet of values of some sort, like I did with pyafq_tractometry, but that seems to maybe not be the case? What outputs should I be looking at and how can I access/view them? Any guidance anyone might be able to provide would be so greatly appreciated. Thank you so much!

Command used:

apptainer run --cleanenv qsiprep-0.19.1.sif \
/home/harrioem/Desktop/qsiprepdata \
/home/harrioem/Desktop/qsiprepdata/derivatives participant \
-w /home/harrioem/Desktop/qsiprepworkdir \
--fs-license-file /home/harrioem/Desktop/qsiprepadmin/FS720license \
--recon-spec mrtrix_singleshell_ss3t_ACT-hsvs \
--output-resolution 1.3 \
--freesurfer-input /home/harrioem/Desktop/qsiprepdata/derivatives/freesurfer

(this did run successfully)

Version:

0.19.1

Environment:

Singularity/apptainer on amazon workspace

Data formatted according to a validatable standard? Please provide the output of the validator:

My input data was BIDS compliant.

Relevant log outputs (up to 20 lines):

N/A (successful run)

Screenshots / relevant information:

If there is any more information I might be able to provide, please let me know.
Any guidance anyone might be able to provide on what files to look for or viewer programs or anything would be so greatly appreciated. Thank you so very much for your help!! (I am truly so grateful for the geniuses on this forum)

2

Hi @emilymharriott,

You should see a .mat file that contains the connectivity matrices as defined by the recon spec. Many softwares (Matlab, Python, R, etc) can load those. That’s the final output of the workflow.

You might also be interested in viewing or doing further processing with the ODFs, such as the normed white matter fod file (.mif), which can be viewed with mrview .

Best,
Steven

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