Hi Hengameh,

sorry, I don't understand most of these questions. We don't have an official release of the hippocampal segmentation software yet, although our development version can be downloaded, which contains the subcortical (including hippocampus) segmentation.

What do you mean by "slide"? Do you mean "slice"? If so, you must give watershed all slices otherwise it won't work at all. And I don't understand 4 - which two volumes do you mean?

cheers, Bruce

On Fri, 18 Nov 2005, hengameh haghighat wrote:

Hello

I have three problems with FreeSurfer software.

1- I don't know how to segment the hippocampus with FreeSurfer software.

For this reason i segmentated the hippocampus with another software (MRIcro) and then gave these slides to FreeSurfer software for measuring volume of hippocampus. The obtained volume was greater than the normal volume. For this reason I made a phantom with the specific volume of 27.142 cm3 to obtained correction factor.

2- In the guide's FreeSurfer it is said when watershed algorithm is corrupted , change the preflooding height to 30% in the setting section of RmSkull tab in expert preference , however I didn't get any result.

3- when an analyze file including one slide or all of the taken slides are given to the FreeSurfer software the watershed algorithm is corrupted and the volume is not calculated .

4- How much is the difference between the volume of the subject brain with FreeSurfer software (Albert) and the obtained volume in FreeSurfer software? how have you obtained it's correction factor?

I would be thankful if you help me in this matter. I look forward to hearing for you soon

Sincerely Yours

-- Tehran University of Medical Sciences (www.tums.ac.ir)

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