Several open-source software allow measurements of brain gyri, some of them are FreeSurfer, Siena (FSL), SPM, MIPAV (NIH). Which one do you think is better accepted by the scientific community?
Dear Ernesto !
I don't know the MIPAV software (maybe someone else can comment on that), but in general I would say both FreeSurfer and FSL are widely accepeted in the scientific community, they are well-maintained and have a good forum to ask questions and for support. I haven't used SPM that much, but it is well-known as well. You might have a look into the literature, where people were comparing e.g. FreeSurfer and FSL if you are not sure which one to use regarding performance. For example we have compared hippocampal volumes, and in our case FreeSurfer performed better than FSL (compared to manual segmentation). But be aware that segmentations with these packages can take a few hours for one brain !
Regards, Bernd
I agree with Bernd! From my experience, FreeSurfer gives you the best segmentation results, but it requires good hardware and takes several hours to process. I personally use FSL to explore data and then if I need to get more serious with it, I use FreeSurfer for optimal segmentation. Both are widely used in the scientific literature and give good overall results. You might want to check this paper also: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714773/
Thank you Paulo, does FreeSurfer has a manual to learn it; or is it needed to take special course?
They are offering courses, have a look here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription
However, I think the websites are already quite useful and explaining a lot. From my personal point of view, I would start to play around with the software and some data and then a course might be helpful to supplement and to have specific questions. Mailing list and forum are really good and helpful as well.
I would like to throw out one more vote for Freesurfer. It is by far the most widely used program to estimate cortical thickness. Freesurfer and FSL both do a fine job estimating volume, but some methodological comparisons suggest that Freesurfer does a bit better job.
Thanks a lot Brian for your comment, I will implement its usage in our MRI unit. Regards.
But be aware that FreeSurfer doesn't run on a normal Windows system (if you prefer that), unless you use a virtual machine.
Thank you Bernd I will try to install on Linux and/or Mac system.
Hey Ernesto
I would go for Freesurfer too, that really is one of the most widely used and freely accessible software out there.
However, just like any other automated method, I'd pay a lot of attention to every step (especially when you first use it) and look at each subject segmentation carefully, especially if you don't have a huge sample. Indeed, Freesurfer segmentation (just like every other software) sometimes mistakes and you end up with very inappropriate values. In my experience, it is often the case in the medial temporal lobe, for the segmentation of the entorhinal/parahippocampal cortices and hippocampus.
There are multiple ways to correct the segmentation (manually cleaning up the skull, adding control points to help segment the white matter, ...), and you should be able to find the documentation on the FS website.
Best,
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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