I’m trying to get images of post-mortem brains, some from cadavers, some excised, into standard space. I’m new to Freeview, so I’m not sure if I’m doing something wrong, or my expectations are wrong. I find the Transform Volume tool easy to use to get an image
that is correctly rotated, and shifted so that the image is centered in the frame. The image looks great in the Freeview panes.
Upon saving and then opening the output nifti, I find the rotational changes have stuck, but the image is as off-center as the original, with the coronal and axial off towards one side, and the sagittal not at the midbrain.
When saving the image, I click on ‘Save Volume as…’, leave the boxes unchecked (‘do not resample’’, and ‘crop to’ ), I modify the file name, then click OK. I don’t click on ‘Move Center…’, I don’t check ‘Apply to all…’.
My expectation is that the image would not only be correctly rotated, but that it would also be centered. Is that the expected behavior here?
I’ve tried the ‘Move Center to Current Cursor Location’, and the Apply to all visible volumes, and see no difference. The off-centeredness is visible in multiple viewers, FSLEyes, MRIcroGL, and ROIEditor. The directions seem so simple and clear, I’m just baffled.
Thank you!