Fmriprep: no html file created when running fmriprep

[acsouza]

Hi!
I’m new with fmriprep and in order to understand the tool I’m running it in a public dataset. It passed BIDS validator and terminal seems to freeze at:

resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 1 -subjid sub-01 -sd /out/freesurfer *
200427-22:17:01,353 nipype.workflow INFO:
* [Node] Running “_autorecon_surfs0” (“smriprep.interfaces.freesurfer.ReconAll”), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 1 -subjid sub-01 -sd /out/freesurfer *
200427-22:17:01,388 nipype.interface INFO:
* resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 1 -subjid sub-01 -sd /out/freesurfer

Recon-all finishes without errors (recon-all.log):
recon-all -s sub-01 finished without error at Mon Apr 27 22:16:54 UTC 2020

However, no report html file is created neither sub-01/func

Here is the original data directory tree:
ds000116/
├── CHANGES
├── README
├── dataset_description.json
├── participants.tsv
├── sub-01
│ ├── anat
│ │ ├── sub-01_T1w.nii
│ │ └── sub-01_inplaneT2.nii
│ └── func
│ ├── sub-01_task-auditoryoddballwithbuttonresponsetotargetstimuli_run-01_bold.nii
│ ├── sub-01_task-auditoryoddballwithbuttonresponsetotargetstimuli_run-01_events.tsv
│ ├── sub-01_task-auditoryoddballwithbuttonresponsetotargetstimuli_run-02_bold.nii
│ ├── sub-01_task-auditoryoddballwithbuttonresponsetotargetstimuli_run-02_events.tsv
│ ├── sub-01_task-auditoryoddballwithbuttonresponsetotargetstimuli_run-03_bold.nii
│ ├── sub-01_task-auditoryoddballwithbuttonresponsetotargetstimuli_run-03_events.tsv
│ ├── sub-01_task-visualoddballwithbuttonresponsetotargetstimuli_run-01_bold.nii
│ ├── sub-01_task-visualoddballwithbuttonresponsetotargetstimuli_run-01_events.tsv
│ ├── sub-01_task-visualoddballwithbuttonresponsetotargetstimuli_run-02_bold.nii
│ ├── sub-01_task-visualoddballwithbuttonresponsetotargetstimuli_run-02_events.tsv
│ ├── sub-01_task-visualoddballwithbuttonresponsetotargetstimuli_run-03_bold.nii
│ └── sub-01_task-visualoddballwithbuttonresponsetotargetstimuli_run-03_events.tsv

and that’s how I’m running the script:
fmriprep_docker /Users/souza/Documents/postdoc\ /test-database\ /external/ds000116/ /Users/souza/Documents/postdoc\ /test-database\ /external/derivatives/ participant --participant-label 01 --fs-license-file /Users/souza/Documents/postdoc\ /freesurfer-license.txt --ignore slicetiming

I appreciate any help.
Ana

[mgxd]

how long have you been processing? the recon-all step can take up a large chunk of time.

[acsouza]

I left it for 3 days. And recon-all.log gives this message (although the terminal was not released yet):
recon-all -s sub-01 finished without error at Mon Apr 27 22:16:54 UTC 2020
I'm running on MacBook Pro 2,3 GHz Intel Core i5. 8 GB 2133 MHz LPDDR3.

[effigies]

Can you try adding -vv to the fmriprep-docker command? The increased verbosity should make it clearer what fMRIPrep thinks is happening.

[acsouza]

Hi,
These are the last updates on the terminal. The last line is like this for 16 hours.

200430-23:14:53,945 nipype.workflow INFO:
[Job 386] Completed (fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern).
200430-23:14:53,954 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 7.00/7.00, Free processors: 2/2.
200430-23:14:54,589 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/tmp/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
200430-23:14:54,623 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-01 -sd /out/freesurfer
200430-23:14:54,624 nipype.workflow INFO:
[Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 1 -subjid sub-01 -sd /out/freesurfer
200430-23:14:54,628 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-01 -sd /out/freesurfer
200430-23:14:55,956 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 2.00/7.00, Free processors: 1/2.
Currently running:
*fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol

[mgxd]

@acsouza sorry for the delay - it looks like freesurfer is hanging. can you paste the contents of <freesurfer-directory>/sub-01/scripts/recon-all.log? That should hopefully help narrow down the problem.

[acsouza]

Hi Mathias, 
Thank you for your reply. I was able to solve the issue. 
Best regards, Ana 
Em terça-feira, 25 de agosto de 2020 14:13:32 GMT-7, Mathias Goncalves [e-mail] escreveu:

@acsouza sorry for the delay - it looks like freesurfer is hanging. can you paste the contents of /sub-01/scripts/recon-all.log? That should hopefully help narrow down the problem.

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