Add SlicerFreeSurferCommands extension :arrow_right: Add SlicerFreeSurferCommands to SlicerFreeSurfer extension

[benzwick]

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New extension

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[jcfr]

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

[benzwick]

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.

This would be very nice. I might need some hints on how to implement this @pieper.

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

The cortical parcellation option adds more segments but I don't know if these have named labels.

Also since we have the AMPSCZ team at project week we should ask some of them about how neuroimaging researchers might use this.

This is a good idea.

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

One thing to consider is that the existing SlicerFreeSurfer extension doesn't have any external dependencies as far as I'm aware, whereas this SlicerFreeSurferCommands extension depends on FreeSurfer which needs to be installed and configured by the user, takes up about 14 GB of disk space, and can only be installed on Linux/Unix OS (on Windows WSL can be used).

[pieper]

This would be very nice. I might need some hints on how to implement this @pieper.

here's a similar script: https://gist.github.com/pieper/17cf79b8ea852693bde0b63bafbaa74f

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).

[pieper]

The cortical parcellation option adds more segments but I don't know if these have named labels.

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

[benzwick]

I opened a new issue at SlicerFreeSurfer to discuss the merge of SlicerFreeSurfer and SlicerFreeSurferCommands, and the move to the Slicer GitHub organization:

• https://github.com/PerkLab/SlicerFreeSurfer/issues/15

[benzwick]

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.

@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.

[pieper]

@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! 👍

[jcfr]

To move forward with this, I suggest to work on https://github.com/PerkLab/SlicerFreeSurfer/issues/15#issuecomment-1679940955

@benzwick How does that sound ?

[jcfr]

To follow-up, this pull request will not be integrated. Instead the following need to be finalized:

• https://github.com/PerkLab/SlicerFreeSurfer/issues/15