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Add SlicerFreeSurferCommands extension ➡️ Add SlicerFreeSurferCommands to SlicerFreeSurfer extension #1943
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This looks like a very useful extension, thanks 👍
I agree getting this in sooner and getting feedback will be better than trying to spend a lot of time refining everything in this interface.
One thing I think would be very helpful to people though would be to load then results as a segmentation and set the names of the segments.
I thought there were more segments than this, but I believe these are the segment names.
https://github.com/BBillot/SynthSeg/blob/0369118b9a0dbd410b35d1abde2529f0f46f9341/data/labels%20table.txt#L17
Also since we have the AMPSCZ team at project week we should ask some of them about how neuroimaging researchers might use this.
Thanks for the contribution. Since there is already a SlicerFreeSurfer extension, should we consider updating the existing one ? See https://github.com/PerkLab/SlicerFreeSurfer If we move forward with this, we could look into moving the repository into the Slicer the GitHub organization and add an Acknowledgements section. Cc: @lassoan |
This would be very nice. I might need some hints on how to implement this @pieper.
The cortical parcellation option adds more segments but I don't know if these have named labels.
This is a good idea.
One thing to consider is that the existing |
here's a similar script: Regarding existing SlicerFreeSurfer, I think this makes sense to bundle, making it clear that these commands are only available if freesurfer is installed. That is, make it clear to the user at runtime, rather than in documentation, what features would be available if freesurfer is installed along with pointers to the installation instructions (even a button that opens the web page). |
If you don't find it, you could post a link on their issue page. It may be this table: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT |
I opened a new issue at SlicerFreeSurfer to discuss the merge of SlicerFreeSurfer and SlicerFreeSurferCommands, and the move to the Slicer GitHub organization: |
@pieper I've added this feature allowing the segmentation to be loaded as either a LabelMapVolume or a Segmentation. Both use the FreeSurferColorLUT converted to a 3D Slicer color table to assign colors and labels. |
This is great! 👍 |
To move forward with this, I suggest to work on PerkLab/SlicerFreeSurfer#15 (comment) @benzwick How does that sound ? |
To follow-up, this pull request will not be integrated. Instead the following need to be finalized: |
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