2 ms·

Here are a couple Ben Goldacre articles on neuroscience in general: https://www.theguardian.com/commentisfree/2011/sep/09/bad-science-research-error https://ww

Here are a couple Ben Goldacre articles on neuroscience in general: https://www.theguardian.com/commentisfree/2011/sep/09/bad-science-research-error https://www.theguardian.com/commentisfree/2011/sep/09/bad-sc... For fMRI research specifically, I seem to remember that almost all of the analysis software is closed source, and that comparing the readings between software versions isn't actually meaningful even though a lot of papers do so.

acveilleux 10y ago
That's actually the same article on two sites. Itself just a layman's piece on an actual article in Nature Neuroscience.
- Alex3917 10y ago
  Oops, deleted the second link. The reason I didn't link to the original journal article is that JumpCrisscross specifically asked for a source for a layman.
leemailll 10y ago
Actually for fMRI studies most people use matlab and share it. It is not really closed-sourced. But I guess many guys in the field won't bother too much to read the codes from a widely used and well-cited matlab script
- deleted 10y ago
  [deleted]
mattkrause 10y ago
> almost all of the analysis software is closed source This is almost certainly not true. BrainSurfer is closed-source, but almost everything else I can think of is open-source. * SPM is available under the GPL: http://www.fil.ion.ucl.ac.uk/spm/software/ http://www.fil.ion.ucl.ac.uk/spm/software/ * FSL (including the source) is available under their own noncommercial "As-Is" license. FSLView seems to have its own separate GPL license: http://fsl.fmrib.ox.ac.uk/fsldownloads/ http://fsl.fmrib.ox.ac.uk/fsldownloads/ * AFNI used to require (free) registration, but is now GPL: https://afni.nimh.nih.gov/afni/about/legal https://afni.nimh.nih.gov/afni/about/legal * The BIC-MNI tools + source appear to be freely available for free under an "as-is" + attribution license. I only checked a few; please let me know if any are not and I will nag people accordingly: https://github.com/BIC-MNI https://github.com/BIC-MNI * Caret is GPL: http://brainvis.wustl.edu/wiki/index.php/Caret:About http://brainvis.wustl.edu/wiki/index.php/Caret:About * FreeSurfer has its own license which is very open: http://www.freesurfer.net/fswiki/FreeSurferSoftwareLicense http://www.freesurfer.net/fswiki/FreeSurferSoftwareLicense I suspect you're thinking of this, which reported differences between FreeSurfer versions: http://journals.plos.org/plosone/article/comment?id=info%3Adoi%2F10.1371%2Fannotation%2F2054bfcc-614f-4fe0-b1e4-72b6e89ba8e5 http://journals.plos.org/plosone/article/comment?id=info%3Ad... That turned out to be a combination of 1) algorithmic changes 2) Different random seeds (some of these functions use Monte Carlo-like methods), and 3) 32 vs 64 bit platforms.
- mattkrause 10y ago
  Err...I was actually thinking of Brain Voyager, which is closed source and incredibly expensive. However, luckily for me, there is also a closed source package called Brain Surfer(!)

acveilleux 10y ago

That's actually the same article on two sites. Itself just a layman's piece on an actual article in Nature Neuroscience.

Alex3917 10y ago
Oops, deleted the second link. The reason I didn't link to the original journal article is that JumpCrisscross specifically asked for a source for a layman.

leemailll 10y ago

Actually for fMRI studies most people use matlab and share it. It is not really closed-sourced. But I guess many guys in the field won't bother too much to read the codes from a widely used and well-cited matlab script

deleted 10y ago
[deleted]

mattkrause 10y ago

> almost all of the analysis software is closed source This is almost certainly not true. BrainSurfer is closed-source, but almost everything else I can think of is open-source. * SPM is available under the GPL: http://www.fil.ion.ucl.ac.uk/spm/software/ http://www.fil.ion.ucl.ac.uk/spm/software/ * FSL (including the source) is available under their own noncommercial "As-Is" license. FSLView seems to have its own separate GPL license: http://fsl.fmrib.ox.ac.uk/fsldownloads/ http://fsl.fmrib.ox.ac.uk/fsldownloads/ * AFNI used to require (free) registration, but is now GPL: https://afni.nimh.nih.gov/afni/about/legal https://afni.nimh.nih.gov/afni/about/legal * The BIC-MNI tools + source appear to be freely available for free under an "as-is" + attribution license. I only checked a few; please let me know if any are not and I will nag people accordingly: https://github.com/BIC-MNI https://github.com/BIC-MNI * Caret is GPL: http://brainvis.wustl.edu/wiki/index.php/Caret:About http://brainvis.wustl.edu/wiki/index.php/Caret:About * FreeSurfer has its own license which is very open: http://www.freesurfer.net/fswiki/FreeSurferSoftwareLicense http://www.freesurfer.net/fswiki/FreeSurferSoftwareLicense I suspect you're thinking of this, which reported differences between FreeSurfer versions: http://journals.plos.org/plosone/article/comment?id=info%3Adoi%2F10.1371%2Fannotation%2F2054bfcc-614f-4fe0-b1e4-72b6e89ba8e5 http://journals.plos.org/plosone/article/comment?id=info%3Ad... That turned out to be a combination of 1) algorithmic changes 2) Different random seeds (some of these functions use Monte Carlo-like methods), and 3) 32 vs 64 bit platforms.

mattkrause 10y ago
Err...I was actually thinking of Brain Voyager, which is closed source and incredibly expensive. However, luckily for me, there is also a closed source package called Brain Surfer(!)