dsi_studio_autotrack not running

[aazor]

Summary

Tried to run 0.22.0 and unstable 0.22.1
Did not get any output from dis_studio_autotrack. From one of the log files (attached)
slurm-37677449_137.pdf
, it appears that dsi_studio_autotrack attempted to run, but there were errors during the process related to logging and the execution of DSI Studio commands.

Additional details

• QSIPrep version: 0.22.0 and 0.22.1-unstable
• Docker version:
• Singularity version: Singularity/Apptainer Version: 1.1.7

What were you trying to do?

Ran qsiprep, trying to run dis_studio_autotrack to obtain the segmented 56 WM tracts in a CSV file.

What did you expect to happen?

I expected to get 2 directory outputs: qsiprep and qsirecon-DSIStudio (which would have the CSV file with data from the segmented WM tracts). I did a run with an earlier version, which successfully ran through autotrack, and gave a CSV output, but some tracts were missing. I know this was a bug you were working on.

What actually happened?

I only got qsiprep outputs. Did not get any qsirecon-DSIStudio output

Reproducing the bug

[mattcieslak]

Hi @aazor, Could you please add --stop-on-first-crash?

Also, we're splitting up qsiprep into qsiprep and qsirecon, so in the next release you'll have to do a separate apptainer command to run the recon workflow.

[aazor]

Hi @mattcieslak
I had the --stop-on-first-crash flag in the previous attempt. Here is the log file. I had the same outputs.
slurm-37604789_99.pdf

[mattcieslak]

do you know anything about the error at the bottom? cp: cannot stat '/om2/scratch/tmp/aazor/read_proc/sub-READ2043//data/derivatives/qsirecon/sub-READ2043

[aazor]

yes. It's the very last line and attempt at moving my files to another directory out of /scratch

"

Copy data back to final destination

mkdir -p ${output_dir}/qsiprep_${qsiprep_version}/
mkdir -p ${output_dir}/qsirecon_${qsiprep_version}/
cp -rn $scratch/data/derivatives/qsiprep/$subject ${output_dir}/qsiprep_${qsiprep_version}/
cp -n $scratch/data/derivatives/qsiprep/${subject}.html ${output_dir}/qsiprep_${qsiprep_version}/
cp -rn $scratch/data/derivatives/qsirecon/$subject ${output_dir}/qsirecon_${qsiprep_version}/
cp -n $scratch/data/derivatives/qsirecon/${subject}.html ${output_dir}/qsirecon_${qsiprep_version}/

"

But this shouldn't be impacting qsirecon and DSI studio output correct?
Because '/om2/scratch/tmp/aazor/read_proc/sub-READ2043/data/derivatives/qsirecon' doesn't exist.

[aazor]

I also think "qsiprep" did not finish running successfully and therefore ${output_dir} and its subdirectories were not created.

[tsalo]

There are two slashes in the path: /om2/scratch/tmp/aazor/read_proc/sub-READ2043//data/derivatives/qsirecon/sub-READ2043. I think that'll resolve to /data/derivatives/qsirecon/sub-READ2043. Perhaps the double slashes are the source of the problem?