Fmriprep stuck during recon-all

Software Support
1

Summary of what happened:

I am running fmriprep-docker and it is hanging on the following step. I have successfully run fmriprep 24.1 this way for other subjects in the same experiment, and this is the first time I have encountered this issue. The only change is that I was recently forced to update Docker, but I can’t see a clear connection between that and this issue. Any advice or help would be greatly appreciated!

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker /Users/[username]/Experiments/[experimentName]/data \
/Users/[username]/Experiments/[experimentName] \
participant \
--participant-label sub-104 \
--output-space T1w \
--fs-license-file /Applications/freesurfer/7.4.1/license.txt \
-w /Users/[username]/Experiments/[experimentName]/working

Version:

24.1.?

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

2025-01-18 19:41:01,551 [    INFO] resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 7 -subjid sub-104 -sd /out/sourcedata/freesurfer

Screenshots / relevant information:

2

Hi @lovescello and welcome to neurostars!

In the future please use the Software Support post category / template. You can see I edited your post accordingly this time.

How much memory/cpu did you devote to the jobs? Have the jobs timed out and how long have you waited? Does this happen consistently for this subject / other subjects, even after using a fresh working directory?

Best,
Steven

3

Hi Steven,

I apologize for using the wrong category, thank you for correcting it!

I have attempted to run this subject 4 times with fresh working directories. The jobs have never timed out, I have waited 12 hours and they all stick at the same point (resume recon-all). I have not tried running another subject since encountering the issue, so I am trying that now. Sorry for the basic question, but how would I check how much memory/cpu is devoted to the job?

Thank you!

4

Hi @lovescello,

recon-all takes a while, you can try waiting longer.

Docker settings, under “Resources”

image
image1660×1292 216 KB

Best,
Steven

5

Hi Steven,

Screenshot 2025-01-18 at 10.56.15 PM
Screenshot 2025-01-18 at 10.56.15 PM1032×1052 35.5 KB

Thank you! I will try waiting longer. How long should I wait/let it run? In the meantime, here is my Docker info:

6

Hi @lovescello,

I would wait a day. Also, 8gb isn’t a lot of RAM, so it could be possible there are memory issues.

Best,
Steven

7

Hi Steven,

I have now tried it with a different subject and waited over a day and it is still stuck at the same place (resume recon-all). I agree that 8 gb isn’t a lot of RAM, but it seems odd that fmriprep was working on the same computer with the same parameters up until now. Do you have any suggestions for workarounds I can try?

Thank you for your help!

8

Hi @lovescello,

You can try running freesurfer independently outside of fmriprep. If you have access to a compute cluster at your institution it would be better to move to that.

Best,
Steven