4 ms·

FreeSurfer: Open-source software for processing and analyzing brain MRI images

60 points by XzetaU8 5y ago

FL33TW00D 5y ago
I’m extremely impressed with the longevity of FreeSurfer, I just desperately wish it was extensible with different atlases.
- a-dub 5y ago
  it's like what? 10-15 years now?
- riskneutral 5y ago
  What does “extensible with different atlases” mean?
  - ska 5y ago
    The idea predates modern usage, back to 1967: https://en.wikipedia.org/wiki/Talairach_coordinates https://en.wikipedia.org/wiki/Talairach_coordinates, where they were trying to define a common way of referring to structures. In this freesurfer sense it is the result of a training set, where an expert has delineated cortical and/or subcortical structure on a set of one or more images. If you have multiple images and you map them all into the same atlas space, you can derive a probabilistic model from this, or collapse it to a highest likelihood map or whatever you want. The cortical and subcortical labeling algorithms used in freesurfer use such a (probabilistic) atlas as one of the inputs. GP is wishing that they could replace this with a new, presumably improved, version.
- marmaduke 5y ago
  It is extensible if you have the training set. A more recent criticism is that it only uses the curvature of the cortical surface to do its work, whereas more recent atlases such at the Glasser HCP use multimodal data.
  - FL33TW00D 5y ago
    Exactly this, I just want to use it with Glasser or the like but it's not really feasible. And since DKT just doesn't capture what we need, FreeSurfer gets left behind.
marmaduke 5y ago
In a few hours with FreeSurfer, you can go from a raw MRI image to a structured labeled set of data identifying the geometry of a subjects brain structures. One of the interesting hacks is to inflate the cortical surface to a sphere which enables nonlinear registration to the accuracy of human experts.
dingosity 5y ago
Hmm. This is the first open source program I've seen that requires a license key.
fluidcruft 5y ago
FreeSurfer is actually NOT open source. https://surfer.nmr.mgh.harvard.edu/registration.html https://surfer.nmr.mgh.harvard.edu/registration.html https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCorTechsLicense https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCorTechs... Edit: and downvotes don't change reality. It's great software, but it's not open source.
- dangom 5y ago
  Here's the source: https://github.com/freesurfer/freesurfer https://github.com/freesurfer/freesurfer. It's open (according to most people's understanding of open), but it's not free for commercial use likely because of IP reasons and to avoid conflicts of interest when receiving funding from the NIH to continue development.
  - keithnz 5y ago
    not free for commercial? the license is https://github.com/freesurfer/freesurfer/blob/dev/LICENSE.txt https://github.com/freesurfer/freesurfer/blob/dev/LICENSE.tx... . My reading of it says you can use it for commercial use and make derivative commercial products under your own license terms. The only thing it says is it is not FDA approved and should really only be used for research purposes, but you can do what you want, we don't accept any responsibility for your use of the software.
    - fluidcruft 5y ago
      Large portions of FreeSurfer are covered by a different license which includes non-free terms such as > (d) such use, reproduction, making of derivative works, display and distribution of the software is limited to non-commercial internal research and educational purposes by not-for-profit entities; > (e) you may not use Freesurfer in research that is sponsored by a commercial entity; > (g) you agree that this License Agreement may be terminated at any time by notice posted on Licensor applicable website if any contributor to Freesurfer with the legal right to do so demands that or compels Licensor to terminate this license.
  - 5y ago
hatmatrix 5y ago
This seems like a very specific piece of software so I'm wondering why it has garnered enough votes to make it to the front page - is there something particular about this code base or software program that I should be paying attention to?
- reom_tobit 5y ago
  I’m just here for the phrase “Skullstripping”. Jokes aside, I think niche software like this is everything HN is about (at least to me). I have no knowledge of MRIs, beyond getting on last year, but seeing this had made me start to research how I would get my brain data back from the NHS to play around with it and see what idiocy I can get up to.
- dangom 5y ago
  It's one of the most popular software packages within the brain MR community. There are many alternatives, but FreeSurfer is one of the first and most robust packages that allows researchers to segment (divide the imaged tissue into classes: white matter, gray matter, cerebral spinal fluid), parcellate (add labels to different brain regions), and generate cortical surface models that can be used to quantify cortical thickness across the human brain. FreeSurfer is also very influential because it offers a bunch of utility tools for doing analysis/stats on brain images and cortical surfaces, and these tools can be easily combined with other popular neuroimaging software packages.
- ska 5y ago
  I think, like blender, it overlaps with interests of a lot of people who end up here - an people have done some very cool projects with it. It's also a good example of something pretty rare: a long lived, decently made and supported project that facilitates a lot of other peoples research.
clueless 5y ago
I got to know Iman personally a little, and he's easily one of the smartest people I know
caycep 5y ago
I have not really opened Freesurfer in ages...but unless they've really put effort into modernizing it, it's "UI" is best described as...."grad student" at best. Still, it's better than AFNI...

60 points by XzetaU8 5y ago

I’m extremely impressed with the longevity of FreeSurfer, I just desperately wish it was extensible with different atlases.

a-dub 5y ago
it's like what? 10-15 years now?
riskneutral 5y ago
What does “extensible with different atlases” mean?
- ska 5y ago
  The idea predates modern usage, back to 1967: https://en.wikipedia.org/wiki/Talairach_coordinates https://en.wikipedia.org/wiki/Talairach_coordinates, where they were trying to define a common way of referring to structures. In this freesurfer sense it is the result of a training set, where an expert has delineated cortical and/or subcortical structure on a set of one or more images. If you have multiple images and you map them all into the same atlas space, you can derive a probabilistic model from this, or collapse it to a highest likelihood map or whatever you want. The cortical and subcortical labeling algorithms used in freesurfer use such a (probabilistic) atlas as one of the inputs. GP is wishing that they could replace this with a new, presumably improved, version.
marmaduke 5y ago
It is extensible if you have the training set. A more recent criticism is that it only uses the curvature of the cortical surface to do its work, whereas more recent atlases such at the Glasser HCP use multimodal data.
- FL33TW00D 5y ago
  Exactly this, I just want to use it with Glasser or the like but it's not really feasible. And since DKT just doesn't capture what we need, FreeSurfer gets left behind.

marmaduke 5y ago

In a few hours with FreeSurfer, you can go from a raw MRI image to a structured labeled set of data identifying the geometry of a subjects brain structures. One of the interesting hacks is to inflate the cortical surface to a sphere which enables nonlinear registration to the accuracy of human experts.

dingosity 5y ago

Hmm. This is the first open source program I've seen that requires a license key.

fluidcruft 5y ago

FreeSurfer is actually NOT open source. https://surfer.nmr.mgh.harvard.edu/registration.html https://surfer.nmr.mgh.harvard.edu/registration.html https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCorTechsLicense https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCorTechs... Edit: and downvotes don't change reality. It's great software, but it's not open source.

dangom 5y ago
Here's the source: https://github.com/freesurfer/freesurfer https://github.com/freesurfer/freesurfer. It's open (according to most people's understanding of open), but it's not free for commercial use likely because of IP reasons and to avoid conflicts of interest when receiving funding from the NIH to continue development.
- keithnz 5y ago
  not free for commercial? the license is https://github.com/freesurfer/freesurfer/blob/dev/LICENSE.txt https://github.com/freesurfer/freesurfer/blob/dev/LICENSE.tx... . My reading of it says you can use it for commercial use and make derivative commercial products under your own license terms. The only thing it says is it is not FDA approved and should really only be used for research purposes, but you can do what you want, we don't accept any responsibility for your use of the software.
  - fluidcruft 5y ago
    Large portions of FreeSurfer are covered by a different license which includes non-free terms such as > (d) such use, reproduction, making of derivative works, display and distribution of the software is limited to non-commercial internal research and educational purposes by not-for-profit entities; > (e) you may not use Freesurfer in research that is sponsored by a commercial entity; > (g) you agree that this License Agreement may be terminated at any time by notice posted on Licensor applicable website if any contributor to Freesurfer with the legal right to do so demands that or compels Licensor to terminate this license.
- 5y ago

hatmatrix 5y ago

This seems like a very specific piece of software so I'm wondering why it has garnered enough votes to make it to the front page - is there something particular about this code base or software program that I should be paying attention to?

reom_tobit 5y ago
I’m just here for the phrase “Skullstripping”. Jokes aside, I think niche software like this is everything HN is about (at least to me). I have no knowledge of MRIs, beyond getting on last year, but seeing this had made me start to research how I would get my brain data back from the NHS to play around with it and see what idiocy I can get up to.
dangom 5y ago
It's one of the most popular software packages within the brain MR community. There are many alternatives, but FreeSurfer is one of the first and most robust packages that allows researchers to segment (divide the imaged tissue into classes: white matter, gray matter, cerebral spinal fluid), parcellate (add labels to different brain regions), and generate cortical surface models that can be used to quantify cortical thickness across the human brain. FreeSurfer is also very influential because it offers a bunch of utility tools for doing analysis/stats on brain images and cortical surfaces, and these tools can be easily combined with other popular neuroimaging software packages.
ska 5y ago
I think, like blender, it overlaps with interests of a lot of people who end up here - an people have done some very cool projects with it. It's also a good example of something pretty rare: a long lived, decently made and supported project that facilitates a lot of other peoples research.

clueless 5y ago

I got to know Iman personally a little, and he's easily one of the smartest people I know

caycep 5y ago

I have not really opened Freesurfer in ages...but unless they've really put effort into modernizing it, it's "UI" is best described as...."grad student" at best. Still, it's better than AFNI...