Hi All,
I'm a new Freesurfer user, and I'm trying my best to pick it up on my own with the wealth of documentation available. Unfortunately, I can't seem to find any mention of this particular problem in the wiki or in the archives of this newsletter, so I hope someone can help. Please forgive me, I'm still learning, and I may not know the correct terminology for some items; I will try to describe the problem as best I can.
I'm attempting to simply view a set of DICOM images (T1 format) with TkMedit before I convert and/or process them at all, just to make sure they are loading properly. The 120 slices load fine using the Philips proprietary DICOM viewer, but for some reason when I load the image in TkMedit, a strange series of displacements occur.
In each plane at least 1 or 2 "lines" appear, dividing the brain so that the entire image has been shifted (by perhaps a voxel or half a voxel) beyond this line. This shift can happen in any direction (anterior/posterior, lateral/medial, superior/inferior). For instance, when viewing the image in the sagittal plane, one of these lines appears at approximately the pre-central gyrus, traveling straight "up and down" so that everything in front of the line is shifted as though I had scrolled 1 additional slice sagitally through the brain. (In the lateral/medial direction, the temporary "z" axis when viewing the image sagitally, not the true superior/inferior z axis). This was immediately visually obvious because some slices of the brain have starkly different contrast, so when different parts of the brain were being shown at different slices, it really popped out. However, other similar lines are simply shifted "up/down" or "forward/back" one voxel, making them less obvious but still problematic. All of these lines are constant, in the same location for each slice.
I am really not sure what is causing this, although my first tentative guess is to wonder whether the images were perhaps acquired at an oblique angle and TkMedit is trying to compensate for that in some way. Beyond that though, I really do not have any guesses. Does anyone have any ideas about what might be going on, and how I might fix it?
I apologize if I have stated any of this poorly. Any help or pointers in the right direction would be appreciated tremendously.
Thank You,
-Patrick