When I try to run fmriprep in singularity for a particular study (this script was adapted from another study) - fmriprep doesn’t run, but I don’t get any particular error - just blank output. Has anyone experienced this before? I don’t know how to fix this issue without any error output? Here is …

Thanks for this feedback, that’s what I was thinking, but what I’ve written doesn’t seem to stop the blank screen hanging. I ran the following and it still hangs with no output (I also tried removing the skip_bids_validation and no joy)… Here is my updated command. Is there some issues with it? S…

I am not sure if that will make a difference, but what I do is to give a specific name to the mounted directory, for example here is a typical command I use: singularity run -B /scratch/jsein/BIDS:/work,$HOME/.templateflow:/opt/templateflow --cleanenv /scratch/jsein/my_images/fmriprep-21.0.2.simg \…

What kind of memory/cpu usage are you devoting to the job?

I haven’t made any changes here regarding memory. Do you think this might be forcing it to fail? I have tried to update my code to the following as per the suggestions above and it still appears to be failing. Also went here and tried all of the suggestions. I do appear to be able to complete al…

One detail: there is a typo in your command just above: -B ${localnifty}:/workd should be: ${localnifty}:/work , or /work/derivatives/fmriprep-v22.0.2/should be /workd/derivatives/fmriprep-v22.0.2/ I also think that you should specify how much memory and cpu you plan to use to be sure to have enou…

Thanks I’ve allocated the following tags… –low-mem --n-cpus 6 --mem-mb 50000 None of these seem to make any difference. Still hanging, should I add anything else to reduce my memory allocations?

What do you see in the log as an output of your command and at which stage does it hangs? The memory allocation looks ok to me. Also, I just noticed in your data hierarchy: your dataset is not bids valid as you are missing one layer: the ses-01/ subdirectory. You should have: local_nifty/ sub-…

[image] AustinBipolar: –n-cpus 6 --mem-mb 50000 These will not change how much memory/cpu is devoted to the job, just how much memory/cpu fMRIPrep will use out of what is available to it. That is, you can specify --mem-mb 50000, but if you only give fMRIPrep 20GB, then that flag won’t be doin…

Hi Steven and Jsein, Firstly, I am so sorry this is such a drama, but I just can’t think of what I am missing here. I spent the morning cleaning up my files to make sure I had enough space to run this analysis and it’s still stalling. Originally, I was submitting a bash script job via sbatch on o…

Singularity and fmriprep

jsein November 2, 2022, 7:34am 2

Hi,

It seems that you are not binding any folder to your singularity container (option -B which should appear before ${fmriprep} in your singularity call.

An explanation for this binding was given in another thead by @Steven :