Hi fmriprepers! Please could you advise why I can’t seem to produce carpet plots with fmriprep 1.4.1rc4 and including MNI152NLin2009cAsym as an output option? This was run in Jupyter Notebook and sent to a HPC using sbatch - the command was: sbatch --mincpus=6 --time=24:00:00 --job-name=fmriprep …

Hi @JoffJones , I just pushed a PR addressing this. Meanwhile, could you test whether reordering your --output-spaces would fix the problem? In particular, can you place any surface-template space to the end of the list? --output-spaces MNIPediatricAsym:cohort-1:res-2 T1w MNI152NLin6Asym:res-2 MNI…

I am having the same problem with 1-4-1rc5, except I usually get an OSError: handle is closed at the end of processing. [image] FMRIPREP error: OSError: handle is closed I’m getting this error now with 1-4-1rc5, but am assuming it’s pretty okay, except that I…

Are you reusing the working directory? Looks like a problem with old results. If you don’t want to remove all the cached results, would you first try deleting /CALM_BIDS_New_2/derivatives/fmriprepwork/fmriprep_wf/single_subject_001_wf/func_preproc_task_rest_wf/carpetplot_wf? That said, I would very…

I’m not re-using my working directory, using a temporary directory each time, and I’ve heard from @monicathieu that this error persists in stable 1-4-1. Results in no carpetplots despite sometimes showing no errors to report! in the .html report. I have occurences of both types (no errors and error…

Similarly, I ran fmriprep without any pre-existing working directories - so the only thing I can think of is if there is a problem when using multiple templates, perhaps if fmriprep is going to the working directory for the results normalised to the child template?

Okay, thanks for the feedback. It seems like we need to have a deeper look as soon as possible. EDIT: https://github.com/poldracklab/fmriprep/issues/1721

Just to confirm that the error persists in 1.4.1 and here’s the associated output: Node Name: fmriprep_wf.single_subject_001_wf.func_preproc_task_rest_wf.carpetplot_wf.select_std fmriprep1.4.1 carpet plot error.txt (630.9 KB) Thanks for your help

Wondering @oesteban whether this would affect outputs in some way I should be concerned about? I’m not able to tell specifically from the github issues, though I assumed not. I’m currently running > 1200 subjects through a cluster and would just hit pause on that if I’m going to have to re-run them…

Hi @oesteban , thanks for looking into this. I was just wondering if the plan is to patch this in 1.5.0 and if you have an estimated release date for this? Many thanks, Joff

Hi @JoffJones , yes, that is the only outstanding issue holding up 1.5.0. I can’t give you an estimation, but I don’t expect it to take much longer than one week.

Hi @oesteban , I never would have thought to try that but it seems to have fixed the problem! I now have a nice carpet plot in my fmriprep report and no errors to report. Thanks for looking into this!

Fmriprep carpet plot error

Ursula_Tooley July 30, 2019, 12:43pm 2

I am having the same problem with 1-4-1rc5, except I usually get an OSError: handle is closed at the end of processing.