Summary of what happened:
Hi there! I am using qsiprep on my DTI images and the pipeline executed without errors. However, in the QC output, there are only QC figures for T1 brain mask, dwidenoise, T1 registration, and the carpetplot. I did not see QC plot for biascorrection. I wonder if I am missing anything. I pasted my commandline below.
Command used (and if a helper script was used, a link to the helper script or the command generated):
/opt/conda/envs/qsiprep/bin/qsiprep /data /out participant --participant-label 6002 -w /work --nprocs 6 --omp-nthreads 6 --mem 24576 --output-resolution 1.5 --skip-bids-validation --fs-license-file /opt/freesurfer/license.txt
Version:
1.0.0rc2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
I skipped bids validation.
Relevant log outputs (up to 20 lines):
[environment]
cpu_count = 20
exec_env = "apptainer"
free_mem = 113.6
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.5"
templateflow_version = "23.1.0"
version = "1.0.0rc2.dev0+g789be41.d20241119"
[execution]
bids_dir = "/data"
bids_database_dir = "/work/20250916-004514_e0e6daaf-a5ef-4729-b73f-c05095cf79ef/bids_db"
bids_description_hash = "e088309ff0c5aa3ed2727e3bf9fa706a6a9fd39ad90bfcdb1be9f10ab95db306"
boilerplate_only = false
sloppy = false
debug = []
layout = "BIDS Layout: .../data | Subjects: 1 | Sessions: 1 | Runs: 0"
log_dir = "/out/logs"
log_level = 25
low_mem = false
notrack = false
output_dir = "/out"
reports_only = false
run_uuid = "20250916-004514_e0e6daaf-a5ef-4729-b73f-c05095cf79ef"
participant_label = [ "6004",]
processing_list = [ "6004:001",]
skip_anat_based_spatial_normalization = false
templateflow_home = "/home/users/meishai/.cache/templateflow"
work_dir = "/work"
write_graph = false
[workflow]
anat_modality = "T1w"
anat_only = false
anatomical_template = "MNI152NLin2009cAsym"
b0_threshold = 100
b0_motion_corr_to = "iterative"
b0_to_t1w_transform = "Rigid"
b1_biascorrect_stage = "final"
denoise_after_combining = false
denoise_method = "dwidenoise"
distortion_group_merge = "none"
dwi_denoise_window = "auto"
dwi_no_biascorr = false
dwi_only = false
fmap_bspline = false
force_syn = false
hmc_model = "eddy"
hmc_transform = "Affine"
ignore = [ "fieldmaps",]
infant = false
intramodal_template_iters = 0
intramodal_template_transform = "BSplineSyN"
subject_anatomical_reference = "first-alphabetically"
longitudinal = false
no_b0_harmonization = false
output_resolution = 1.5
pepolar_method = "TOPUP"
separate_all_dwis = false
shoreline_iters = 2
use_syn_sdc = false
spaces = "MNI152NLin2009cAsym"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
memory_gb = 24.576
nprocs = 6
omp_nthreads = 6
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = false
[seeds]
master = 63553
ants = 30746
numpy = 19723
[execution.derivatives]
[execution.dataset_links]
raw = "/data"
templateflow = "/home/users/meishai/.cache/templateflow"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false