Size of ground truth images in the multicoil brain test set

[mersad95zd]

Hi,

Thanks for maintaining this forum. The ground-truth data for the multicoil brain test set is not to be released, but is it possible that you release the ground-truth image size for each test sample?

I'm asking because to save memory during training, one (if not resorting to another option) has to crop input samples. One way is to crop according to the ground-truth image size. In this case, we need ground-truth image sizes for the test set because if we don't crop at inference, a performance drop occurs (due to resolution mismatch).

An alternative would be cropping to the maximum image size of the test set. So if you can't release all image sizes, releasing the maximum size of the test set would also be appreciated. Thanks in advance!

[mmuckley]

Hello @mersad95zd, this information is already in the dataset in the HDF5 attrs field and is returned to you as batch.crop_size. You can see its usage here in the standard LightningModule:

fastMRI/fastmri/pl_modules/varnet_module.py

Lines 131 to 137 in ce9a8ef

	# check for FLAIR 203
	if output.shape[-1] < batch.crop_size[1]:
	crop_size = (output.shape[-1], output.shape[-1])
	else:
	crop_size = batch.crop_size
	output = transforms.center_crop(output, crop_size)

This shows how it is extracted from the file:

fastMRI/fastmri/data/transforms.py

Line 353 in ce9a8ef

crop_size = (attrs["recon_size"][0], attrs["recon_size"][1])

There is some extra handling because some FLAIR203 images from the dataset had incorrect cropping information in their headers.

[mersad95zd]

Thanks a lot @mmuckley for your prompt response! I totally missed that, especially these lines:

fastMRI/fastmri/data/mri_data.py

Lines 352 to 356 in ce9a8ef

	recon_size = (
	int(et_query(et_root, rec + ["x"])),
	int(et_query(et_root, rec + ["y"])),
	int(et_query(et_root, rec + ["z"])),
	)

[mmuckley]

Ah yes - I might have retrieved from there instead. Sorry, it's been awhile since I wrote this code :).

[tasik34]

Unfortunately, we can't release specific ground-truth image sizes check correct images dimensions on the website. However, the maximum image size for the test set is 320x320. Hope this helps with your memory-saving approach!

[mmuckley]

This is not correct - the image size data is available in the metadata, as outlined in my earlier answer.

[mersad95zd]

Thanks for the follow-up! My issue was addressed by @mmuckley 's comment 2 years ago! I'll close it now (should've done so back then).