Perhaps by using a box or sphere, centred around particular coordinates, or using anatomical features as boundaries?
I believe that if you run Freesurfer on your structural images you will get a hypothalamus mask for each subject. You could then uses this as an individual mask or put then into atlas space to get an average mask.
Hi, that sounds perfect thanks, as I wanted to use individual masks in the first instance. I will look into using Freesurfer then!
You could try our new online platform for automatic MRI brain analysis.
Our web based pipeline is called "volBrain" and can be accessed at this address:
http://volbrain.upv.es
volBrain is able to produce volumetric information of different brain tissues/structures in a fully automatic way in around 15 minutes. The way it works is very simple; you have just to register as a new user in the system and to upload a single anonymized compressed T1w brain MRI in nifti format. You will receive an email with a pdf/csv summarising the results and you will be able also to download the resulting label files and images in your user area using your account.
Our aim is to provide a simple and free tool that can be used no matter where you are without any installation or computer requirements. Since we want to make the tool available to the higher possible number of users, a limit of 5 cases per day/user has been set.
We encourage you to register in the system and to use it. We will be very grateful if you can provide us your comments/suggestions in order to improve the system.
Good luck in your research!!
Jose V. Manjon and Pierrick Coupe
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