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`sct_fmri_compute_tSNR` does not detrend the data before computing the standard deviation. From what I've seen online, it is important to detrend the data before computing the std (the mean should sti…
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## Summary
Instead of FAST, use SynthSeg segmentations for 5TT/GMWMI generation
## Additional details
FAST isn't great, and we already have SynthSeg outputs from QSIPrep
## Next steps
Her…
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Within the master and gh-pages branches there are still references to the ohbm2018- VMs and containers which come from repronim or other "users and organizations", e.g. as the ones from myyoda and mih…
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- (fsl) fast
- (fsl) flirt
- (fsl) fnirt
- ...
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## Checklist
#### Question/suggestion about FSL or an FSL analysis
I watched the recent apple event. Does FSL work on the new computers apple released?
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There is a [work in progress branch](https://github.com/alistair23/linux/tree/5.4-rM2-2.2.x-imx-deep-sleep) to add deep sleep support to the 5.4 kernel.
The problem is that deep sleep (called lpsr)…
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### Objective
SignIt does 2 external queries at start [sw.js#L43-L47](https://github.com/lingua-libre/SignIt/blob/master/sw.js#L43-L47). Since Lingualibre.org will be phased out, migration to Wikid…
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### Describe the bug
When fsl BET is used for skull stripping or brain extraction, the neck regions from the anatomical image does not get removed for some subjects.
As you can see in this example,…
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e.g.
```shell
root@76bcdd396583:/opt/repronim/simple_workflow/scripts# dpkg-query -S /usr/lib/fsl/5.0
fsl-5.0-eddy-nonfree, fsl-5.0-core: /usr/lib/fsl/5.0
```
which makes total sense. I guess ste…
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### What would you like to see added in fMRIPrep?
I've come to the realization that maintaining ``--fs-no-reconall`` is costly, and more worryingly, provides a space for users to create different var…