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Neural-Systems-at-UIO / QuickNII

https://quicknii.readthedocs.io
MIT License
7 stars 3 forks source link

Export slices from command line #26

Closed paulbrodersen closed 1 year ago

paulbrodersen commented 1 year ago

Hi, thanks for creating QuickNII and making it available for the wider community.

I am using QuickNII together with DeepSlice. DeepSlice seems to be working well for my data, so usually all I have to do is load the DeepSlice XML file into QuickNII, and hit "Export Slices". Since I have a large number of brains to process, and the next step in my pipeline involves a manual validation step anyway (that would also catch any registration issues), I am tempted to automate this process. Does QuickNII support exporting slices from command line given a proper XML file containing the registration results, or could this feature be reasonably easy implemented? I am imagining something along the lines of

java -cp Serv Serv ABA_Mouse_CCFv3_2017_25um.cutlas --xml /path/to/deepslice_results.xml --export

(I am using the linux patch, which works great).

Tevemadar commented 1 year ago

You can try NIISlicer from https://github.com/Tevemadar/QuickNII-extras/tree/master/Java As it requires a NIfTI volume to slice, it may be worth adding that VisuAlign contains such volumes.

paulbrodersen commented 1 year ago

Thanks for the quick reply. I will try that out.