I suggest to bump up priority this ticket: saving a project becomes very time consuming after DICOM data has been consolidated in a local directory as nrrd files. All volumes are written back on disk in their entirety -- every time! This also messes up time stamps and creates chances of data corruption (and wears on SSDs etc..)

@nick_slizer if you rename the volume node before saving then the filename will match that and subsequent saves won't re-save the file if the volume node hasn't changed.

What circumstance leads to the volumes being written back each time?

Thanks for tips. I found the problem, sort of.

First, I couldn't actually reproduce the scenario of the OP, so maybe this ticket is altogether invalid as of now?

Second, I should have checked the log files and MRML files: for some reason, the file name of a cropped volume had been corrupted, but only in its VolumeArchetypeStorage node, not in the Volume node. The corruption consists of a doubling of the ".nrrd" suffix, so that the file got named "X.nrrd.nrrd" instead of "X.nnrd". I fixed that in a text editor and voila the problem has gone away.

The problem was actually flagged in the Data module when I hovered the mouse over the volume X and it also lit up the error icon in the lower right corner (but it turns to "red" usually, need to change my habits).

I played with the Crop module to see whether I could tease it into doubling the suffix, but didn't succeed. Renaming the volume didn't work for me either, thus detour over text editor.

@fedorov, can you see if this is still an issue for you? If not this can be closed.

@nick_slizer thanks for testing. There had been an issue with doubled extensions like that but I'd thought it was resolved. Maybe the issue you saw came from an earlier build or something.

Thanks for heads-up on known earlier doubling issue, I'm using 4.9.0-2018-04-06 r27131, will investigate further and report in separate thread.