Hi,
In reconstructing some normal adult MPRAGEs, I've had a couple of different fairly large errors that I haven't been able to fix: (1) In a handful of subjects, more than half of the brain is lost, I think during the skullstripping step (ie, isn't present on the white matter or brainmask volumes later). This seems to be primarily on scans from a 3T Siemens with a 32channel head coil. I have tried adding control points, but this doesn't help. (2) In another handful of subjects, a large portion of the cerebellum is designated as cortex, and is labeled on the aseg maps.
Any suggestions on how to fix these two types of problems?
thanks, Nicole
Hi Nicole If you upload some examples we will take a look. What version as you running? Have you checked the accuracy of the talairach.xfm?
Cheers Bruce
On Jun 8, 2012, at 11:19 AM, Nicole Senecal senecaln@mail.med.upenn.edu wrote:
Hi,
In reconstructing some normal adult MPRAGEs, I've had a couple of different fairly large errors that I haven't been able to fix: (1) In a handful of subjects, more than half of the brain is lost, I think during the skullstripping step (ie, isn't present on the white matter or brainmask volumes later). This seems to be primarily on scans from a 3T Siemens with a 32channel head coil. I have tried adding control points, but this doesn't help. (2) In another handful of subjects, a large portion of the cerebellum is designated as cortex, and is labeled on the aseg maps.
Any suggestions on how to fix these two types of problems?
thanks, Nicole
-- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
Both are uploaded. FI137 is the missing brain from surfs and wm.mgz, and OH120 is the cerebellum in -aseg. We're running freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.
thanks, Nicole
On Fri, Jun 8, 2012 at 8:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Nicole If you upload some examples we will take a look. What version as you running? Have you checked the accuracy of the talairach.xfm?
Cheers Bruce
On Jun 8, 2012, at 11:19 AM, Nicole Senecal senecaln@mail.med.upenn.edu wrote:
Hi,
In reconstructing some normal adult MPRAGEs, I've had a couple of
different fairly large errors that I haven't been able to fix:
(1) In a handful of subjects, more than half of the brain is lost, I
think during the skullstripping step (ie, isn't present on the white matter or brainmask volumes later). This seems to be primarily on scans from a 3T Siemens with a 32channel head coil. I have tried adding control points, but this doesn't help.
(2) In another handful of subjects, a large portion of the cerebellum is
designated as cortex, and is labeled on the aseg maps.
Any suggestions on how to fix these two types of problems?
thanks, Nicole
-- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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