Hello,
We have a relatively small FOV in our study because we mostly scan kids. Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc labels, where the very back of the brain gets labeled as orbitofrontal cortex. Is there a way to remedy this (other than increasing the FOV for subsequent subjects)? E.g. manually relabeling the affected regions?
I'm pretty new to FreeSurfer, so I apologize in advance if this questions is naive.
Thanks!
Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital
Hi Maria
if the brain wraps from back to front then it can't be recovered. Nothing to do with the analysis - the imaging data itself is corrupted.
sorry Bruce On Thu, 6 Jun 2013, Maria Kharitonova wrote:
Hello,
We have a relatively small FOV in our study because we mostly scan kids. Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc labels, where the very back of the brain gets labeled as orbitofrontal cortex. Is there a way to remedy this (other than increasing the FOV for subsequent subjects)? E.g. manually relabeling the affected regions?
I'm pretty new to FreeSurfer, so I apologize in advance if this questions is naive.
Thanks!
Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Maria, if the warp around is such that the wrapped part of the brain ends up outside the brain but on the other side of the FOV, you can maybe fix it partially (e.g., if the frontal cortex is wrapped to the back but not into the occipital cortex). You would just need to copy the respective rows from the back to the front of the image before any processing of the data (use MRIread in Matlab). However, the data will be unreliable; this may only help with alignment of images etc., but I wouldn't try to analyze the data in any way. Caspar
2013/6/6 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Maria
if the brain wraps from back to front then it can't be recovered. Nothing to do with the analysis - the imaging data itself is corrupted.
sorry Bruce On Thu, 6 Jun 2013, Maria Kharitonova wrote:
Hello,
We have a relatively small FOV in our study because we mostly scan kids.
Sometimes we scan adults with the same protocol, though, and after looking through the adults' reconned brains, I've noticed wrap-around on some brains. For one subject it's particularly bad; it affects aparc labels, where the very back of the brain gets labeled as orbitofrontal cortex. Is there a way to remedy this (other than increasing the FOV for subsequent subjects)? E.g. manually relabeling the affected regions?
I'm pretty new to FreeSurfer, so I apologize in advance if this
questions is naive.
Thanks!
Maria Kharitonova, Ph.D. Postdoctoral Research Fellow Laboratories of Cognitive Neuroscience Boston Children's Hospital
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Maria Kharitonova