Hi there, I have run fmriprep (Docker-based) on a Resting State fMRI dataset (ie. participant level, re-using existing FreeSurfer results, SDC) with version 21.0.2 and later on version 21.0.4. The output results were sensibly different, principally -based on the QC reports- for the BOLD carpet plo…

[image] jhuguetn: Differences are very subtle but still looks like there’s some sort of stochastic process that affects having a perfectly reproducible output. The fmriprep.toml config. file which registers the seeds used by the pipeline show different values (probably randomly generated). So I…

On the whole, I’d say these don’t look dramatically different, and agree with @jsein that it’s likely mostly a plotting issue combined with expected levels of non-determinism. We have recently fixed the random ordering of the correlation matrix, which I believe was in the 22.1.0 release. As to the …

Thanks both for your prompt replies @jsein and @effigies , Will carefully check those interesting links you shared, @jsein . I suspect that you’ll probably see high correlations (low correlation distance) everywhere except right along the boundary of the brain mask, where some voxels switch to in/o…

I wonder how much change on those masks you would get if you were running the same version of fmriprep twice on the same subject. Could you try that?

[image] jhuguetn: That’s good to know, would you then advise to switch to the 22.1 series on this regard? It depends on your situation. If 21.0.2 has been working for most of your dataset and 21.0.4 fixes issues with the rest of your dataset, then it makes sense to upgrade to 21.0.4. If you …

I wonder how much change on those masks you would get if you were running the same version of fmriprep twice on the same subject. Could you try that? I did it and there are indeed result changes across re-runs of the same version (eg. brain masks, confounds plots and even the intensity values of …

Fmriprep results differ across versions of 21.0 series

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jsein March 7, 2023, 3:13pm 2

Hi,

At first sight, what looks different is the display of the carpet plot and the correlation matrix between matrices, mostly due to different ordering of their elements (order of voxels or order of confounds).

This discussion has some elements than are interesting about this topic:

and this cited paper also:

There is also this conversation on this topic:

This post is also speaking about this topic:

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