Hi,
I'm trying to use the simulated MEG data provided on the MEGSIM-Portal (http://portal.mind.unm.edu/megsim/) for evaluation purposed. To construct a forward model I'm trying to extract the cortical surface from the MRI data provided.
For this, I converted the DICOM files to a NIfTI file, imported it into BrainVISA, and tried to use the "T1 Pipeline 2007" to perform the segmentation. Unfortunately, the segmentation does not work, i.e., when using the default settings the pipeline stops at "Split Brain Mask" with the following error:
I assume this error occurs because the brain mask is not extracted corretly; it looks like this:
The rest of the mask is empty. I assume this problem is related to the histogram analysis. When I change "Vip Histogram analysis" to "Histogram analysis" I get a mask which is too large, i.e., it covers part of the skull.
Any tips on how to fix these problems, which I assume are caused by a problem with the histogram analysis, are highly appreciated. I used BrainVISA before and so far the segmentation always worked without much tweaking.
Best,
Martin
PS: I tried both BrainVISA V 3.2 and 4.0, both have the same problem
Problems segmenting MRI image from "MEGSIM"
- riviere
- Site Admin
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- Location: CEA NeuroSpin, Saint Aubin, France
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Re: Problems segmenting MRI image from "MEGSIM"
Hi,
We cannot really see the brain on the slices you show here, so we cannot see the contrasts in the brain and get an idea of what caused the problem. However it is generally linked to a failure of the bias correction, before the histogram analysis.
Please search the forum for classical problems, for instance:
http://brainvisa.info/forum/viewtopic.p ... 446&p=5268
http://brainvisa.info/forum/viewtopic.p ... 443&p=5261
http://brainvisa.info/forum/viewtopic.p ... t=22&p=127
etc.
Denis
We cannot really see the brain on the slices you show here, so we cannot see the contrasts in the brain and get an idea of what caused the problem. However it is generally linked to a failure of the bias correction, before the histogram analysis.
Please search the forum for classical problems, for instance:
http://brainvisa.info/forum/viewtopic.p ... 446&p=5268
http://brainvisa.info/forum/viewtopic.p ... 443&p=5261
http://brainvisa.info/forum/viewtopic.p ... t=22&p=127
etc.
Denis
- Jean-Francois Mangin
- Posts: 337
- Joined: Mon Mar 01, 2004 10:24 am
- Location: Neurospin, CEA, France
- Contact:
Re: Problems segmenting MRI image from "MEGSIM"
Maybe the histogram analysis failed, you should try to modify one of the parameter
for histogram sampling.
for histogram sampling.