SAMRI
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IBT-FMI
Small Animal Magnetic Resonance Imaging via Python.
I would like to see implemented DTI support in addition to fMRI / structural. Can provide test dataset
Curently, we are testing if all imports work by including [this snippet](https://github.com/IBT-FMI/SAMRI/blob/fa3ab993259524ac77c69171713226fb8f7110d5/samri/plotting/__init__.py#L1-L7) in all modules' `__init__.py`. This is quite annoying, since it loads all imports from a module even only...
One thing that got lost in the recent preprocessing update is that the workdir is now subdivided in what appears to be indices of the BIDS dataframe, rather than more...
As of 93b083bb7122379b38704069092d9c9d9c4525df datasets produced by `samri.pipelines.reposit()` pass the [BIDS validator](http://incf.github.io/bids-validator/). However, there's still come non-fatal errors, most prominently that we are missing a `SliceTiming` parameter. This might also help...
Our diagnosis tool for stimulus evoked activity and measurement quality/stability uses FSL's `melodic`. Though the MELODIC guide [recommends the input be preprocessed](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC#Pre-Stats) the pipeline still fails as soon as the...
Since we're making progress on fetching, maybe it would be a good idea to add fetch capabilities for dummy BIDS data (iirc the BIDS people publish a dummy dataset). This...
The [recently contributed correlation matrix function](https://github.com/IBT-FMI/SAMRI/blob/8143d761135a66f802aff6120589352932a1ad8f/samri/plotting/examples.py#L312) seems to not work properly. It produces the following plot:  Not least of all, it took a bit of fixing to get it...
SAMRI can now generate seed-based connectivity plots, however, the seed regions of interest might be at slightly different positions and of slightly different shapes/sizes between subjects, at least. A useful...
trying to emerge samri with the following, in a container, using gentoo stage 3 docker image as base: ``` emerge --sync emerge dev-vcs/git emerge --noreplace --verbose eselect-repository eselect repository enable...
using samri container: https://gin.g-node.org/asmacdo/opfvta-singularity test data: https://zenodo.org/records/3831124 and following call: `apptainer run /project/4180000.41/to_run/opfvta.sing SAMRI generic-prep -m 'DSURQE_100micron_mask.nii.gz' -o . samri_bidsdata-0.3/bids 'DSURQE_100micron_average.nii.gz' > log ` I get errors at the `get_s_scan`...