17 is the intensity value for left hippocamus, and 53 for the right hippocamus.  Then you can view  with tkmedit ( to view aseg.mgz) for more clearance. Then use matlab  to extract this label base on the intensities value. 


Azeez Adebimpe



Date: Mon, 26 Nov 2012 13:48:09 +0100
From: andrea.tateo@virgilio.it
To: ayobimpe2004@hotmail.com
Subject: R: RE: [Freesurfer] Info FreeSurfer

Hi  Azeez Adebimpe,


thanks for your quick answer.

I open the text file that you recommended me.

What means these three numbers in the following string:

17 Left_Hippocampus 1.20 0.0 80    ?

How can I use these information in MatLab?



Andrea Tateo




----Messaggio originale----
Da: ayobimpe2004@hotmail.com
Data: 26-nov-2012 13.19
A: <andrea.tateo@virgilio.it>
Ogg: RE: [Freesurfer] Info FreeSurfer

Hi Andrea
You cant restrict ouput of the freesurfer to only hippocamus but after the segmentation you can select the hippocamus both right and left base on intensity value ( check this doc inside mri subfolder:  aseg.auto_noCCseg.label_intensities.txt). You can use matlab or any program to extract the hippocamus.


Azeez Adebimpe



Date: Mon, 26 Nov 2012 13:06:48 +0100
From: andrea.tateo@virgilio.it
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Info FreeSurfer


 Hello,

I am working on segmentation of the hippocampus and I need a comparing method.

I am approaching for the first time to FreeSurfer method.



I would like your courteous help.

I have three questions for you:

1 - I have input a MRI-image.nii showing all head. As output I would like a binary image showing only left and right hippocampus. I used the following command:

###

mri_convert FILE_NAME.nii path/directory/NAME_OUTPUT.mgz

recon-all -s SUBJECT_name -autorecon-all

###


How can I extract the required binary image?

2 - Is it possible to comput only hippocampus region (to reduce the processing time)?

3 - Is it possible to give as input only an ristrected region of the subject's head?


Best regards

Andre Tateo



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