Summary of what happened:
I am trying to run qsirecon 1.1.1, using a .yaml with “mrtrix_5tt_fast” for ACT tractography. It runs successfully and generates streamline outputs, but I just noticed that it isn’t generating the FAST-based 5tt output, and when I look at the tckgen command in the work dir, there is no “-act” argument. There is also no recon_anatomical_wf in the work dir.
When I run the same command but using a .yaml with “mrtrix_5tt_hsvs”, it does generate a 5tt output file, and I can see that tckgen uses “-act”
Command used (and if a helper script was used, a link to the helper script or the command generated):
qsirecon /data/bids/derivatives/qsiprep /data/bids participant \
--input-type qsiprep \
--recon-spec /scripts/mrtrix_multishell_msmt_ifod2fastTEST.yaml \
--fs-subjects-dir /data/bids/derivatives/freesurfer \
--fs-license-file /scripts/freesurfer_license.txt \
-w /data/work-qsirecon \
--write-graph --stop-on-first-crash --verbose --verbose --notrack \
--nthreads 10 --omp-nthreads 10 --resource-monitor
Where the mrtrix_multishell_msmt_ifod2fastTEST.yaml contains:
anatomical:
- mrtrix_5tt_fast
name: mrtrix_multishell_msmt_TEST
nodes:
- action: csd
input: qsirecon
name: msmt_csd
parameters:
fod:
algorithm: msmt_csd
max_sh:
- 8
- 8
- 8
mtnormalize: true
response:
algorithm: dhollander
qsirecon_suffix: MRtrix3_ifod2act-FAST
software: MRTrix3
- action: tractography
input: msmt_csd
name: track_ifod2
parameters:
sift2: {}
tckgen:
algorithm: iFOD2
max_length: 250
min_length: 30
power: 0.33
quiet: true
select: 50000.0
use_5tt: true
use_sift2: true
qsirecon_suffix: MRtrix3_ifod2act-FAST
software: MRTrix3
space: T1w
Version:
qsirecon 1.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
Run via apptainer
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