Hi!

I have a large set of T1-scans from different sites which I have skull-stripped GM-extracted (i.e. I have a set of GM-maps) that are all in native space, no warping has been preformed. That means that some of the brains are pretty far of the matrix-space center.

I am going to run augmentations on these so it is important that they somewhat overlap in space and since I will run rotational augmentations they will also be clipped if they are not in the center of space. I tried this:

1) I wanted the template to have dimensions divisible by 32 for deep learning purposes :

3dZeropad -RL 192 -AP 224 -IS 192 -prefix new_template.nii.gz MNI152_2009_template_SSW.nii.gz

Since the template has the dims 193, 229, 193 the zero-padding doesn't change much and the the template brain is pretty much in the center after this operation which is fine

2) Now I want my data to have the same dimensions so I ran:

3dAllineate -cmass -warp shift_only -base ../new_template.nii.gz -source 28336_1_MR_T1_struc_GM.nii.gz -prefix ../test_out/test.nii.gz

The data now has dims 192,224,192, the brains are centered and it looks good. But the file-size is 3 times larger so i suspect there is some interpolation going on. Is my command as simple as it can be for my purpose or should I add some flags if my goal is to change the resolution and have the brain at the center of volume?

Because I don't want them to be aligned and matched, just to move each subject's T1 so that the center of mass-overlap and give it the same 192,224,192 grid. If that makes sense.

Thanks!



Edited 6 time(s). Last edit at 09/23/2020 09:10AM by Robin.