Hello everyone,
I encountered an unexpected issue after running fmripost-aroma. The functional derivative images such as *.aggrDenoised_bold.nii.gz , *.nonaggrDenoised_bold.nii.gz , and *.orthaggrDenoised_bold.nii.gz were not stored in the func folder under each subject’s directory.
├── dataset_description.json
├── logs
│ ├── CITATION.bib
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
├── sub-01
│ ├── figures
│ │ ├── sub-01_task-rest_desc-about_bold.html
│ │ ├── sub-01_task-rest_desc-aroma_bold.svg
│ │ ├── sub-01_task-rest_desc-metrics_bold.svg
│ │ ├── sub-01_task-rest_desc-normalization_bold.svg
│ │ ├── sub-01_task-rest_desc-summary_bold.html
│ │ ├── sub-01_task-rest_space-MNI152NLin6Asym_desc-aroma_bold.svg
│ │ ├── sub-01_task-rest_space-MNI152NLin6Asym_desc-metrics_bold.svg
│ │ ├── sub-01_task-rest_space-MNI152NLin6Asym_res-02_desc-about_bold.html
│ │ ├── sub-01_task-rest_space-MNI152NLin6Asym_res-02_desc-normalization_bold.svg
│ │ └── sub-01_task-rest_space-MNI152NLin6Asym_res-02_desc-summary_bold.html
│ ├── func
│ │ ├── sub-01_task-rest_desc-aroma_metrics.json
│ │ ├── sub-01_task-rest_desc-aroma_metrics.tsv
│ │ ├── sub-01_task-rest_desc-aroma_timeseries.tsv
│ │ ├── sub-01_task-rest_desc-melodic_components.nii.gz
│ │ ├── sub-01_task-rest_res-2_desc-melodic_mixing.tsv
│ │ ├── sub-01_task-rest_space-MNI152NLin6Asym_res-02_desc-melodic_components.nii.gz
│ │ └── sub-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
│ └── log
│ ├── 20250322-172031_594c8693-ecfc-48aa-9a25-591d7f4885da
│ │ └── fmripost_aroma.toml
│ └── 20250322-174752_bcfca69d-48ea-4d30-b831-bdda0dea8ddb
│ └── fmripost_aroma.toml
├── sub-01.html
Command used (and if a helper script was used, a link to the helper script or the command generated):
Below is the shell script for running fmripost-aroma:
docker run --rm -it \
-v /media/dyyang/WD6TB/fmriprep_work/image:/data \
-v /media/dyyang/WD6TB/fmriprep_work/aroma:/out \
-v /media/dyyang/WD6TB/fmriprep_work/prep:/prep \
nipreps/fmripost-aroma \
/data /out participant \
--derivatives fmriprep=/prep \
--participant-label 01
I have assigned right template in the output space, below is shell script for running fmriprep:
#!/bin/bash
bids_root_dir=/media/dyyang/WD6TB/fmriprep_work/image
bids_output=/media/dyyang/WD6TB/fmriprep_work/prep
fs_license=/media/dyyang/WD6TB/fmriprep_work/license.txt
subjlist=("01" "02")
for subj in ${subjlist[@]}; do
fmriprep-docker $bids_root_dir $bids_output participant \
--participant-label $subj \
--output-spaces MNI152NLin6Asym:res-02 \
--fs-license-file $fs_license
done
Version:
fMRIPost-AROMA version 0.0.10
fmriprep 24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
Ubuntu 22.04.5 LTS
Docker version 27.5.1
Relevant log outputs (up to 20 lines):
[environment]
cpu_count = 20
exec_env = "singularity"
free_mem = 55.8
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.9.2"
templateflow_version = "24.2.2"
version = "0.0.10"
[execution]
bids_dir = "/data"
bids_database_dir = "/tmp/work/20250322-174752_bcfca69d-48ea-4d30-b831-bdda0dea8ddb/bids_db"
bids_description_hash = "e77aff4995fa9ceb1836e6359389013cf76a894bb0feaa63ecdfe95d7118c2b4"
boilerplate_only = false
sloppy = false
debug = []
layout = "BIDS Layout: .../data | Subjects: 2 | Sessions: 0 | Runs: 0"
log_dir = "/out/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = true
track_carbon = false
country_code = "CAN"
output_dir = "/out"
aggr_ses_reports = 4
reports_only = false
run_uuid = "20250322-174752_bcfca69d-48ea-4d30-b831-bdda0dea8ddb"
participant_label = [ "01",]
templateflow_home = "/home/fmripost_aroma/.cache/templateflow"
work_dir = "/tmp/work"
write_graph = false
[workflow]
err_on_warn = false
melodic_dim = 0
ignore = [ "fieldmaps",]
slice_time_ref = 0.5
spaces = "MNI152NLin6Asym"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 20
omp_nthreads = 8
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = false
[seeds]
master = 32888
ants = 9210
numpy = 61078
[execution.derivatives]
fmriprep = "/prep"
[execution.dataset_links]
input = "PosixPath('/data')"
templateflow = "PosixPath('/home/fmripost_aroma/.cache/templateflow')"
fmriprep = "PosixPath('/prep')"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
Screenshots / relevant information:
Interestingly, fmripost-aroma completed without displaying any error messages. Even when I specified the fmriprep derivative folder as the output destination, the .nii files were still not stored in the designated folder.
Has anyone encountered a similar issue or can provide advice on how to resolve this? Appreciated!
David