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SABS-R3-projects / Paint4Brains

A brain MRI segmentation tool that provides accurate robust segmentation of problematic brain regions across the neurodegenerative spectrum. The methodology is generalisable to perform well with the typical variance in MRI acquisition parameters and other factors that influence image contrast.
https://www.sabsr3.ox.ac.uk/software-projects
BSD 3-Clause "New" or "Revised" License
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Things to work on #29

Closed brennanaba closed 3 years ago

brennanaba commented 4 years ago
brennanaba commented 4 years ago

Adjust intensity (slider) Extraction slider. Region name and colour. Select region through name - Manual preprocessing before segmentation (and after). Itai Investigate preprocessing histogram normalisation - Itai Add a progress bar when it is segmenting - Hardware selection button needs more info. - Estimate how long it would take to segment by bench marking machine. - Reduce computational time - Andrei (Recreate QuickNAT in lite/tf 2.0 implementation) Open software without brain Further scientific validation. (Freesurfer and manually labelled) Intercraneal volume normalization Calculate volumes for same patient within short timespan Write the grant request for David - Andrei

Now complete

Select brain slice with mouse wheel. Add an undo button Add a redo button Automatic preprocessing before segmentation

brennanaba commented 4 years ago

Adjust intensity (slider) Extraction slider. Itai Manual preprocessing before segmentation (and after). Itai Investigate preprocessing histogram normalisation - Itai Add a progress bar when it is segmenting - Hardware selection button needs more info. - Estimate how long it would take to segment by bench marking machine. - Reduce computational time - Andrei (Recreate QuickNAT in lite/tf 2.0 implementation) Open software without brain (I don't like this) Further scientific validation. (Freesurfer and manually labelled) Intercraneal volume normalization Calculate volumes for same patient within short timespan

Now complete

Region name and colour. Select region through name Select brain slice with mouse wheel. Add an undo button Add a redo button Automatic preprocessing before segmentation Write the grant request for David

AndreiRoibu commented 4 years ago

**### Now complete

brennanaba commented 4 years ago

Add a progress bar when it is segmenting - Reduce computational time - Andrei (Recreate QuickNAT in lite/tf 2.0 implementation) Further scientific validation. (Freesurfer and manually labelled) Intercraneal volume normalization Calculate volumes for same patient within short timespan - Can have a go at this - Andrei Toolbar is not very intuitive - UX work? - might be worth asking (when hovering over toolbar, show what everything does - maybe a balloon with some help information to make things clear)

MRI Cron - another opensource brain software - have a library of atlases - might be cool for added functionality. Pre-loaded atlases might be a good functionality to allow people to compare atlas based vds non-atlas based stuff. ***

Now complete

Region name and colour. Select region through name Select brain slice with mouse wheel. Add an undo button Add a redo button Automatic preprocessing before segmentation Manual preprocessing after segmentation. Itai - feature already present Write the grant request for David Manual preprocessing before segmentation Investigate preprocessing histogram normalisation - Itai* Adjust intensity (slider) Extraction slider. ItaHardware selection button needs more info. - Estimate how long it would take to segment by bench marking machine. - Andrei - make note on times Making different views views available when drawing different ROI - medium term task (Show all views, maybe with one big main and 2 smaller secondaries at the sides, showing in real time what happens on the 2ndary planes what is being done on the main plane) Have x,y,z on top showing slice number (display coordinate, not the slice information - easy for making notes and keeping track of that - information of particular voxel you are hovering on; GE to check again if there are any bugs - confirmed it is there - maybe make it a bit clear)

AndreiRoibu commented 4 years ago
AndreiRoibu commented 4 years ago

Further scientific validation. (Freesurfer and manually labelled) - couldn't purchase original dataset - going for Hypothalamus one instead.

Intercraneal volume normalization

Calculate volumes for same patient within short timespan - Can have a go at this - Andrei

Look into paper submission - Several journals with paper templates have been identified.

Generate documentation - sphinx works but documentation generated isn't great. Might use it as starting point for manual at a later date. ****

MRI Cron - another opensource brain software - have a library of atlases - might be cool for added functionality. Pre-loaded atlases might be a good functionality to allow people to compare atlas based vds non-atlas based stuff. ***

Reduce computational time - Andrei (Recreate QuickNAT in lite/tf 2.0 implementation)*** - time consuming, and other issues take priority

brennanaba commented 3 years ago

Outdated