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.ta...@virgilio.it To: ayobimpe2...@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: ayobimpe2...@hotmail.com Data: 26-nov-2012 13.19 A: <andrea.ta...@virgilio.it> 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.ta...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
