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
Ogg: RE: [Freesurfer] Info FreeSurfer
Hi AndreaYou 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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