SAMRI
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IBT-FMI
Small Animal Magnetic Resonance Imaging via Python.
Hi @TheChymera I was trying to build this into a Singularity container and got... almost there. I get an error because the Science overlay no longer has scikit-image. Any thoughts...
In Nibabel get_data() is deprecated in favor of get_fdata(). The code in SAMRI I believe uses get_data. Test example (conversion of Bruker to Bids) started to work when I changed...
As discussed here → https://github.com/con/opfvta-replication-2023/issues/18
We (BIDS maintainers) are trying to see if we can improve the quality of the average README in BIDS dataset. Those tend to be pretty thin and are missing some...
Hi @TheChymera, Have a question... I do not have access to a Gentoo environment. Our HPC is Centos07 and I've read through all the deps etc., that are required and...
According to the BIDS specification the run ticker should only be incremented for the same modality: https://bids-specification.readthedocs.io/en/latest/99-appendices/09-entities.html#run Currently we increment it indiscriminately inside each datatype (func/anat/dti): https://github.com/IBT-FMI/SAMRI/blob/eef1f40b2ce732b71539f2cbdfdbfed8591598e5/samri/pipelines/extra_functions.py#L915
While pre-processing resting state fMRI data, I tried to limit the processing done in parallel, since my cluster allows only for a limited amount of capacity used. Therefore, I wanted...
Ideally we would like to have a function which can check the registration quality at a glance - to quantitatively compare alternative preprocessing workflows to ours, but also different parameter...
Dear SAMRI experts, I am trying to install SAMRI. I installed gentoo in my home, installed the overlay science in `/home/salma/gentoo/var/db/repos` and tried to emerge samri but I am getting...
https://github.com/IBT-FMI/SAMRI/blob/master/samri/fetch/templates.py#L22 We should look to migrate our template resolution to proper package management (instead of some web download at runtime), similarly to how this was done for the mouse brain...