In the recent versions of Slicer, I am having a hard time exporting a resampled volume from a linear transform. Hardening simply changes the image direction matrix, so does the crop volume (when the image is under a linear transform). I am pretty sure at some point Crop Volume used to create a resam…

This is now implemented. See the thread [image] Creating ROI box markups in image coordinates (rather than anatomical coordinates) Support for posterity this feature is now implemented in slicer, and part of the CropVolume module since Sept 21s. To align yo…

“Crop volume” module resamples the image if Interpolated cropping option is enabled. This behavior has not been changed in the past couple of years. The output volume is placed under the same transform as the input volume, so one thing to pay attention to is that if you want to have a volume with RA…

[image] lassoan: I assume that you need this for reorienting non-clinical scans to canonical orientation. I True, and sometime people want to move data to other programs that does not read the image direction fields of NRRD (like Fiji). So volume needs to be resampled. [image] lassoan: “…

The ROI that “Fit to volume” button (or automatix “Fix” button) creates is aligned with the volume’s voxel axes (to avoid quality loss by default when cropping). That’s why the output volume had non-identity orientation matrix. To get output volume with axes aligned with RAS directions, you can pla…

[image] lassoan: The ROI that “Fit to volume” button (or automatix “Fix” button) creates is aligned with the volume’s voxel axes (to avoid quality loss by default when cropping). That’s why the output volume had non-identity orientation matrix. I think this is where we can provide the lossy, …

@lassoan I added an issue on Slicer to track this: Add an option to more easily resample linear transforms in Crop Volume · Issue #8415 · Slicer/Slicer · GitHub

Resampling a linear transformation

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lassoan (Andras Lasso) May 15, 2025, 5:04am 7

I agree, this feature will make it easier to create an RAS-axis-aligned volume by resampling.

Creating ROI box markups in image coordinates (rather than anatomical coordinates)

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Resampling a linear transformation

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