Hello
I applied the fmriprep-docker on part of OASIS3 dataset (Tw1).
+---anat
| sub-OAS30754_from-fsnative_to-T1w_mode-image_xfm.txt
| sub-OAS30754_from-T1w_to-fsnative_mode-image_xfm.txt
|
+---figures
| sub-OAS30754_desc-conform_T1w.html
| sub-OAS30754_ses-M000_desc-about_T1w.html
| sub-OAS30754_ses-M000_desc-summary_T1w.html
|
+---log
| \---20230612-213034_cb2acfff-335d-4b1c-87f1-a200abb4aeb2
| fmriprep.toml
|
+---ses-M000
| \---anat
| sub-OAS30754_ses-M000_run-01_from-orig_to-T1w_mode-image_xfm.txt
| sub-OAS30754_ses-M000_run-02_from-orig_to-T1w_mode-image_xfm.txt
|
+---ses-M042
| \---anat
| sub-OAS30754_ses-M042_run-01_from-orig_to-T1w_mode-image_xfm.txt
|
+---ses-M078
| \---anat
| sub-OAS30754_ses-M078_run-01_from-orig_to-T1w_mode-image_xfm.txt
|
\---ses-M114
\---anat
sub-OAS30754_ses-M114_run-01_from-orig_to-T1w_mode-image_xfm.txt
Steven
June 13, 2023, 3:35pm
2
Hi @Yasmine ,
You might find this page helpful Outputs of fMRIPrep — fmriprep version documentation
I am guessing based on this that the session number is days since study enrollment for that subject.
fMRIPrep can process T1w and BOLD data, but not PET.
Looks like it crashed because these are not the final outputs. The final preprocessed T1w image (probably what you are looking for) is a NIFTI file (.nii.gz).
Best,
Thank you so much for your response. Is there a way to know why it crashed from the logs folder maybe?
This subject does have a nii.gz. Not all subjects have .nii.gz
+---figures
| sub-OAS30512_ses-M012_desc-about_T1w.html
| sub-OAS30512_ses-M012_desc-conform_T1w.html
| sub-OAS30512_ses-M012_desc-summary_T1w.html
|
+---log
| \---20230612-213034_cb2acfff-335d-4b1c-87f1-a200abb4aeb2
| fmriprep.toml
|
\---ses-M012
\---anat
sub-OAS30512_ses-M012_desc-preproc_T1w.json
sub-OAS30512_ses-M012_desc-preproc_T1w.nii.gz
sub-OAS30512_ses-M012_from-fsnative_to-T1w_mode-image_xfm.txt
sub-OAS30512_ses-M012_from-T1w_to-fsnative_mode-image_xfm.txt
sub-OAS30512_ses-M012_run-01_from-orig_to-T1w_mode-image_xfm.txt
sub-OAS30512_ses-M012_run-02_from-orig_to-T1w_mode-image_xfm.txt
Steven
June 13, 2023, 7:51pm
4
Yes the log files should contain info about the error.
May you please guide me if this (fmriprep toml source file) contains useful info about the issue. I didn’t see errors in the files.
[environment]
cpu_count = 20
exec_docker_version = "24.0.2"
exec_env = "fmriprep-docker"
free_mem = 13.5
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "23.0.0"
version = "23.1.0"
[execution]
bids_dir = "/data"
bids_database_dir = "/tmp/work/20230612-213034_cb2acfff-335d-4b1c-87f1-a200abb4aeb2/bids_db"
bids_description_hash = "4085ba054c5022c6c6559e0c144cc6a0a703f830b74d2344738d8b87f966d4d6"
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: 6 | Sessions: 17 | Runs: 11"
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
output_layout = "bids"
output_spaces = "MNI152NLin2009cAsym:res-native"
reports_only = false
run_uuid = "20230612-213034_cb2acfff-335d-4b1c-87f1-a200abb4aeb2"
participant_label = [ "OAS30512", "OAS30513", "OAS30754", "OAS30755", "OAS30996", "OAS30997",]
templateflow_home = "/home/fmriprep/.cache/templateflow"
work_dir = "/tmp/work"
write_graph = false
[workflow]
anat_only = true
aroma_err_on_warn = false
aroma_melodic_dim = 0
bold2t1w_dof = 6
bold2t1w_init = "register"
cifti_output = false
fmap_bspline = false
force_syn = false
hires = true
ignore = []
longitudinal = false
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 = "MNI152NLin2009cAsym:res-native"
use_aroma = false
use_syn_sdc = false
me_t2s_fit_method = "curvefit"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 20
omp_nthreads = 8
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false
[seeds]
master = 50420
ants = 12982
numpy = 8552
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
Steven
June 13, 2023, 9:23pm
6
No, that file is not useful. Do you have the output from the terminal or job log on the system you ran this command (e.g., a Slurm log if you submit jobs with sbatch)? Was an HTML made for a subject that crashed?
Unfortunately, I closed that terminal. There are three html files in the figures folder. But they just have the following text respectively.
### Anatomical Conformation
* Input T1w images: 5
* Output orientation: RAS
* Output dimensions: 192x256x256
* Output voxel size: 1mm x 1mm x 1mm
* Discarded images: 0
fMRIPrep version: 23.1.0
fMRIPrep command: /opt/conda/envs/fmriprep/bin/fmriprep /data /out participant --skip-bids-validation --anat-only
Date preprocessed: 2023-06-12 21:31:14 +0000
Subject ID: OAS30754
Structural images: 5 T1-weighted
Functional series: 0
Standard output spaces: MNI152NLin2009cAsym
Non-standard output spaces:
FreeSurfer reconstruction: Run by fMRIPrep
Steven
June 13, 2023, 9:43pm
8
The HTML would just be called SUBJECT.html (where SUBJECT is the subject ID) and would be on the base level of the fmriprep output folder.
Can you rerun in terminal?
Also, I would recommend adding a working directory to your command with the -w flag.
I skipped Windows and working with Ubuntu.
