Greetings,
I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a starting point for the model it generates. However, for one seeking to study a structure other than the brain, this can be a concern. Can FreeSurfer/Slicer accommodate data whose source is not an MRI and or of the brain?
This concern also stems from the file entitled "SlicerTraining06_vtkFreeSurferReaders.ppt" provided on a Slicer site that has about a dozen tutorials for Slicer 2.6 (this is one of them). On Slide #25, entitled 'Determining label numbers in an ASEG file', there is a list of the first 30 sections created and various parameters. The names of these sections seem to be predetermined (i.e., Left Cerebral-Exterior, Left Cerebral-White-Matter, Left Cerebral-Cortex, etc.). This seems to imply that FreeSurfer/Slicer know what to look for from the onset and thus the segementation is not based solely on quantitative data.
Please let me know if these conclusions are warranted. If I am mistaken, please advise as to why.
Thanks for your time and advice,
Greg
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Hi Greg,
what structures exactly are you interested in? For the most part, we only do brain and brain-related structures (eg, ventricles). I don't know about Slicer, but FreeSurfer only handles T1-weighted MRI data.
doug
Greg Soltis wrote:
Greetings,
I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a starting point for the model it generates. However, for one seeking to study a structure other than the brain, this can be a concern. Can FreeSurfer/Slicer accommodate data whose source is not an MRI and or of the brain?
This concern also stems from the file entitled "SlicerTraining06_vtkFreeSurferReaders.ppt" provided on a Slicer site that has about a dozen tutorials for Slicer 2.6 (this is one of them). On Slide #25, entitled 'Determining label numbers in an ASEG file', there is a list of the first 30 sections created and various parameters. The names of these sections seem to be predetermined (i.e., Left Cerebral-Exterior, Left Cerebral-White-Matter, Left Cerebral-Cortex, etc.). This seems to imply that FreeSurfer/Slicer know what to look for from the onset and thus the segementation is not based solely on quantitative data.
Please let me know if these conclusions are warranted. If I am mistaken, please advise as to why.
Thanks for your time and advice,
Greg
Need a brain boost? Recharge with a stimulating game. Play now! http://club.live.com/home.aspx?icid=club_hotmailtextlink1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Greg,
I think there are certain things you could use, but so much of what we do uses brain-specific information and assumptions that it is going to be rough. What exactly are you trying to achieve?
Bruce
On Mon, 9 Jul 2007, Greg Soltis wrote:
Greetings,
I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a starting point for the model it generates. However, for one seeking to study a structure other than the brain, this can be a concern. Can FreeSurfer/Slicer accommodate data whose source is not an MRI and or of the brain?
This concern also stems from the file entitled "SlicerTraining06_vtkFreeSurferReaders.ppt" provided on a Slicer site that has about a dozen tutorials for Slicer 2.6 (this is one of them). On Slide #25, entitled 'Determining label numbers in an ASEG file', there is a list of the first 30 sections created and various parameters. The names of these sections seem to be predetermined (i.e., Left Cerebral-Exterior, Left Cerebral-White-Matter, Left Cerebral-Cortex, etc.). This seems to imply that FreeSurfer/Slicer know what to look for from the onset and thus the segementation is not based solely on quantitative data.
Please let me know if these conclusions are warranted. If I am mistaken, please advise as to why.
Thanks for your time and advice,
Greg
Need a brain boost? Recharge with a stimulating game. Play now! http://club.live.com/home.aspx?icid=club_hotmailtextlink1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Greg Soltis