Summary of what happened:
Ran fMRIPrep across 50 participants and for the first dozen or so, no problems. Back half of participants seem to have the correct output files but the HTML report only contains two sections ‘About’ and ‘Errors’. There are no errors reported in the HTML report and otherwise everything looks great.
Tried running this again with the --reports-only flag and reports were still missing most of their sections. Any ideas what’s going on here or how to fix these reports? I see all the figures in the figures folder, so seems like it should be possible?
Command used
fmriprep-docker $bids_dir $output_dir participant \
--participant-label $participant_id \
--stop-on-first-crash \
--fs-license-file /Users/fmriuser/license.txt \
--nprocs 12 \
--mem 64000 \
--output-spaces MNI152NLin6Asym:res-02 \
--longitudinal \
-v \
-w /Users/Shared/work \
--image nipreps/fmriprep:25.1.1
Version: fmriprep:25.1.1
Environment: Docker
Relevant log outputs (up to 20 lines):
[environment]
cpu_count = 36
exec_env = "singularity"
free_mem = 60.9
overcommit_policy = "always"
overcommit_limit = "50%"
nipype_version = "1.10.0"
templateflow_version = "24.2.2"
version = "25.1.1"
[execution]
bids_dir = "/data"
bids_database_dir = "/tmp/work/20250714-173519_57ad240c-7912-435e-8e51-9d7b6a5a693f/bids_db"
bids_description_hash = "03c9e8c4ca9927d8cd2f2106548bed6dd41f8a08614ef80a63cbc47e867dc39c"
boilerplate_only = false
sloppy = false
debug = []
fmriprep_dir = "/out"
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "/out/sourcedata/freesurfer"
layout = "BIDS Layout: .../data | Subjects: 1 | Sessions: 2 | Runs: 3"
log_dir = "/out/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
track_carbon = false
country_code = "CAN"
output_dir = "/out"
me_output_echos = false
aggr_ses_reports = 4
output_layout = "bids"
output_spaces = "MNI152NLin6Asym:res-02"
reports_only = false
run_uuid = "20250714-173519_57ad240c-7912-435e-8e51-9d7b6a5a693f"
participant_label = [ "40276",]
templateflow_home = "/home/fmriprep/.cache/templateflow"
work_dir = "/tmp/work"
write_graph = false
[workflow]
anat_only = false
bold2anat_dof = 6
bold2anat_init = "t1w"
cifti_output = false
fmap_bspline = false
force_syn = false
hires = true
fs_no_resume = false
ignore = []
force = []
level = "full"
longitudinal = true
run_msmsulc = true
medial_surface_nan = false
project_goodvoxels = false
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "MNI152NLin6Asym:res-02 MNI152NLin2009cAsym"
use_syn_sdc = false
me_t2s_fit_method = "curvefit"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
memory_gb = 64.0
nprocs = 12
omp_nthreads = 8
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = true
[seeds]
master = 47250
ants = 17452
numpy = 31747
[execution.derivatives]
[execution.dataset_links]
raw = "/data"
templateflow = "/home/fmriprep/.cache/templateflow"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
