Hi
I have a dataset of children who have had hemispherectomy surgery to treat epilepsy. I want to be able to run recon-all on these children. I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere to a template. To mimic a whole brain, I have flipped the single hemisphere over the X-axis and added it to the other half. Thus, I have the original hemisphere, and the "mirrored" hemisphere in one scan. This is my input to recon-all. However, as the scans were acquired some time after surgery, the remaining hemisphere was not perfectly aligned at the midline and expanded / grew into to the empty cranial space, and there are gaps and overlap between the mirrored side and the original side.
Is there a way to run recon-all on the single hemisphere alone, so that I do not have to mirror the brain? Perhaps by supplying a mask, to apply to the FreeSurfer atlases?
Thanks
Kristian
Hi Kristian Can you send us an image to illustrate what you mean? Thanks Bruce
On Feb 11, 2014, at 8:31 PM, Kristian Eschenburg keschenburg90@gmail.com wrote:
Hi
I have a dataset of children who have had hemispherectomy surgery to treat epilepsy. I want to be able to run recon-all on these children. I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere to a template. To mimic a whole brain, I have flipped the single hemisphere over the X-axis and added it to the other half. Thus, I have the original hemisphere, and the "mirrored" hemisphere in one scan. This is my input to recon-all. However, as the scans were acquired some time after surgery, the remaining hemisphere was not perfectly aligned at the midline and expanded / grew into to the empty cranial space, and there are gaps and overlap between the mirrored side and the original side.
Is there a way to run recon-all on the single hemisphere alone, so that I do not have to mirror the brain? Perhaps by supplying a mask, to apply to the FreeSurfer atlases?
Thanks
Kristian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce
Attached here are two screenshots. One is the original template-aligned T1, another is the "mirrored" T1. You can see how in the mirrored image there is overlap of the 2 hemispheres after flipping over the X axis where the central sulcus should be, as well as gaps where the corpus callosum would normally be. I have other subjects where these characteristics are exaggerated or less severe.
Thanks
Kristian
On Tue, Feb 11, 2014 at 6:27 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Kristian Can you send us an image to illustrate what you mean? Thanks Bruce
On Feb 11, 2014, at 8:31 PM, Kristian Eschenburg <
keschenburg90@gmail.com> wrote:
Hi
I have a dataset of children who have had hemispherectomy surgery to
treat epilepsy. I want to be able to run recon-all on these children. I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere to a template. To mimic a whole brain, I have flipped the single hemisphere over the X-axis and added it to the other half. Thus, I have the original hemisphere, and the "mirrored" hemisphere in one scan. This is my input to recon-all. However, as the scans were acquired some time after surgery, the remaining hemisphere was not perfectly aligned at the midline and expanded / grew into to the empty cranial space, and there are gaps and overlap between the mirrored side and the original side.
Is there a way to run recon-all on the single hemisphere alone, so that
I do not have to mirror the brain? Perhaps by supplying a mask, to apply to the FreeSurfer atlases?
Thanks
Kristian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Kristian Eschenburg