Dear all,
I was astonished to see a dramatic drop in file size after using the crop volume module and I don’t understand why.
Here is my original volume volume information:
Now this is my new volume information after crop volume (using a roi to the full frame, B spline and isotropic spacing):
Note that I changed the units in the _iso file manually to the right scale (um instead of mm) before running the crop volume
Now if I save the isotropic file, the space used on disk is 2.3 G compared to 6.3 G for the original file.
How come ?
Many thanks to the community and developpers for help and of course, a great software !
Your second volume (the one generated after cropping) is actually larger than the original one (there are more voxels in Z dimension).
If you choose to compress the file during the save, the file size will be smaller than the memory footprint required to load the file. I presume your original file was not compressed. So that’s probably where the difference is coming from.
For large files like this, I suggest not compressing them. Most of the wait during the save/open operations are actually spend on compressing/uncompressing them as the compression library used is single-threaded.
Thanks Murat,
indeed I expected files larger, not smaller as there are more voxels in the Z dimensions.
In the save tab, I clicked on show options and noticed “compress” was checked. I had forgotten about that option but I probably did this voluntary at some point: I think in my case, storage space is more of a concern than time openning/saving (it s still very fast on my cluster, for files up to 15 GB, I hardly wait).
Perhaps that option should not be “hidden” as I simply forgot about that and went along my pipeline.
S
If you are using SlicerMorph, go to Application Settings->SlicerMorph then check use SlicerMorph customizations and restart Slicer. This will disable compression option for all your volume data.
