Hi:
I processed the T1 volume of a patient... I got bad segmentation of the right hippocampus (see attached images)... How can I correct the segmentation ?...
Sincerely,
Gonzalo Rojas Costa
Hello,
While the segmentation is not so good, the T1 coronal image that you sent suggests that the right medial temporal lobe may not be so normal. I think an underlying abnormality in the temporal lobe is giving rise to the segmentation errors. Perhaps you have other images through the right temporal lobe to confirm this?
Regards,
--Mykol
On Fri, Feb 4, 2011 at 9:33 AM, Gonzalo Rojas gonzalo.rojas.costa@gmail.com wrote:
Hi:
I processed the T1 volume of a patient... I got bad segmentation of the right hippocampus (see attached images)... How can I correct the segmentation ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
Yes... The patient has a resection of the temporal lobe, and I think that produce the problem in the segmentation, but could I correct the segmentation of the hippocampus because I need to get the volume of both hippocampus and the right one will have a big error...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 11:41, Mykol Larvie escribió:
Hello,
While the segmentation is not so good, the T1 coronal image that you sent suggests that the right medial temporal lobe may not be so normal. I think an underlying abnormality in the temporal lobe is giving rise to the segmentation errors. Perhaps you have other images through the right temporal lobe to confirm this?
Regards,
--Mykol
you may need to manually correct it. There's not much we can do when a big chunk of brain is missing On Fri, 4 Feb 2011, Gonzalo Rojas Costa wrote:
Hi:
Yes... The patient has a resection of the temporal lobe, and I think that produce the problem in the segmentation, but could I correct the segmentation of the hippocampus because I need to get the volume of both hippocampus and the right one will have a big error...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 11:41, Mykol Larvie escribió:
Hello,
While the segmentation is not so good, the T1 coronal image that you sent suggests that the right medial temporal lobe may not be so normal. I think an underlying abnormality in the temporal lobe is giving rise to the segmentation errors. Perhaps you have other images through the right temporal lobe to confirm this?
Regards,
--Mykol
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce:
And which freesurfer tool must I use to manually correct it ?... And, how can I generate the aseg.stats file after the manual correction ?...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 14:59, Bruce Fischl escribió:
you may need to manually correct it. There's not much we can do when a big chunk of brain is missing
either tkmedit or freeview, then run autorecon2 and 3 to regenerate the surfaces.
On Fri, 4 Feb 2011, Gonzalo Rojas Costa wrote:
Hi Bruce:
And which freesurfer tool must I use to manually correct it ?... And, how can I generate the aseg.stats file after the manual correction ?...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 14:59, Bruce Fischl escribió:
you may need to manually correct it. There's not much we can do when a big chunk of brain is missing
to fix the lack of wm there you mean? Maybe, or you might put a control point or two in the white matter, depending on how dark it is On Fri, 4 Feb 2011, Gonzalo Rojas Costa wrote:
Hi Bruce:
But, I must edit the wm.mgz file ?...
Sincerely,
Gonzalo Rojas Costa
El 04-02-2011 15:11, Bruce Fischl escribió:
either tkmedit or freeview, then run autorecon2 and 3 to regenerate the surfaces.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Gonzalo Rojas -
Gonzalo Rojas Costa
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Mykol Larvie