Hello,
I am looking in particular for creating lightbox views of BOLD volumetric nifiti data https://fmriprep.org/en/stable/_static/SampleReport/sample_report.html. May I please get any guidance on this? Basically I looked at fsl earlier but it seems really heavy to integrate in our pipeline so I am looking for any lightweight neuroimaging data visualization tools which provides lightbox view
Hi,
Not sure what fmriprep uses, but you can use FSLeyes as a visualization tool for lightbox views - https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/ortho_lightbox_views.html- as well as a nilearn - Plotting brain images - Nilearn. The “mosaic” display model is like what fsl calls lightbox right?
Maybe an R version? MVPA Meanderings: DMCC55B supplemental as tutorial: basic fMRI QC: temporal mean, SD, and tSNR and associated posts/papers gives a bit of an idea of what is possible (plus the code to do it).
are there any tool in neuroimaging data visualization tool in python? other than FSLeyes it seems a bit heavy for our pipelines
This is lightbox (fsleyes.views.lightboxpanel — fsleyes 1.4.6 documentation)
yes I think mosaic display model is the more of general term
Although it may not be apparent from the gallery of example, nilearn is a lightweight python library which can be used to generate mosaic from brain volumes quite flexibly. See this example
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