[HN Gopher] FreeSurfer: Open-source software for processing and ...
___________________________________________________________________
FreeSurfer: Open-source software for processing and analyzing brain
MRI images
Author : XzetaU8
Score : 44 points
Date : 2021-05-03 07:30 UTC (1 days ago)
(HTM) web link (surfer.nmr.mgh.harvard.edu)
(TXT) w3m dump (surfer.nmr.mgh.harvard.edu)
| FL33TW00D wrote:
| I'm extremely impressed with the longevity of FreeSurfer, I just
| desperately wish it was extensible with different atlases.
| marmaduke wrote:
| 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 wrote:
| 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.
| riskneutral wrote:
| What does "extensible with different atlases" mean?
| ska wrote:
| The idea predates modern usage, back to 1967:
| 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.
| a-dub wrote:
| it's like what? 10-15 years now?
| marmaduke wrote:
| 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 wrote:
| Hmm. This is the first open source program I've seen that
| requires a license key.
| clueless wrote:
| I got to know Iman personally a little, and he's easily one of
| the smartest people I know
| hatmatrix wrote:
| 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 wrote:
| 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 wrote:
| 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 wrote:
| 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.
| fluidcruft wrote:
| FreeSurfer is actually NOT open source.
|
| https://surfer.nmr.mgh.harvard.edu/registration.html
|
| 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 wrote:
| Here's the source: 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.
| fluidcruft wrote:
| The Open Source Definition doesn't include "free for non-
| commercial use" licenses.
| keithnz wrote:
| not free for commercial? the license is https://github.com/fr
| eesurfer/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 wrote:
| 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.
___________________________________________________________________
(page generated 2021-05-04 23:01 UTC)