@n_j_davis Pretty sure the JHU white matter atlas is in MNI space. Also has probability thresholds. See https://t.co/dPbI8LtMEp, Fig 7

@ParsaRVN @AFornito @misicbata @goliashf The cortex is PySurfer, and subcortex is made by converting .nii atlas to .vtk mesh (see https://t.co/wTDjs9P8qK) then plotted using PyVista. The files were then overlaid. It's a bit of a hacky script, but the final

@cMadan @NeuroLeyla @CyrilRPernet That's actually a wonderful paper, also your f1000 one https://t.co/HK2vwUiTb9 I personally learnt a lot from the latter too :) thanks @cMadan

RT @TeagueRHenry: Creating "glass brain" figures for manuscripts has been one of my least favorite processes, just due to the fiddly softwa…

RT @TeagueRHenry: Creating "glass brain" figures for manuscripts has been one of my least favorite processes, just due to the fiddly softwa…

RT @TeagueRHenry: Creating "glass brain" figures for manuscripts has been one of my least favorite processes, just due to the fiddly softwa…

RT @TeagueRHenry: Creating "glass brain" figures for manuscripts has been one of my least favorite processes, just due to the fiddly softwa…

Creating "glass brain" figures for manuscripts has been one of my least favorite processes, just due to the fiddly software I used. But I just found https://t.co/kMXfyX3Zc4, which is a great tutorial about using ITK-Snap and Paraview to make glass brains.

@JoCutler8 Hope that helps! Other great software available of course, but that's my workflow. You could also check out @cMadan's awesome guide to 3D visualisations as well: https://t.co/XaLjnsX4rQ

@Kanad_Mandke @esdalmaijer @rogierK See the appendix of https://t.co/dPbI8LteOR for some segmented animal MRIs that can be used for 3D printing

@esdalmaijer @rogierK I use already segmented voxel data, and then build a surface using the procedure I developed here: https://t.co/dPbI8LteOR That paper also provides links to data for some other species that I haven't 3D printed yet (see Fig 5).

Our Research Assistant Chris would like to show his appreciation for the people who have made it easy to visualise structural and functional MRI data. Cheers @cMadan (https://t.co/XjHI9s4NEC) and whoever is behind user "3d_printed_brain" on instructables.

@eplebel I have some movies as figures in this tutorial paper https://t.co/r2Qh8DlkDI

@alie_astrocyte @wrong_whale @SusanLeemburg Most of my own collection is different humans (aging, patients). However, in a tutorial paper I link to a few different species: https://t.co/r2Qh8D3JMa @R3RT0's @BrainCatalogue is more comprehensive, has MRIs

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

@MattOldach @WiringTheBrain @StrictlyStat @neuroconscience Check out this brief guide: https://t.co/5ZsQiH1rJc

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

Useful tool for comparative scientists.

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZ…

RT @cMadan: The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZ…

RT @cMadan: The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZ…

RT @akiraoc: Have used this for a paper currently under review. It's an awesome guide for those looking for better ways of visualising imag…

RT @cMadan: The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZ…

RT @cMadan: The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZ…

RT @cMadan: The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZ…

RT @akiraoc: Have used this for a paper currently under review. It's an awesome guide for those looking for better ways of visualising imag…

Have used this for a paper currently under review. It's an awesome guide for those looking for better ways of visualising imaging data. https://t.co/0YnoTRfUHt

The guide cited is here: "Creating 3D visualizations of MRI data: A brief guide" https://t.co/r2Qh8D3JMa https://t.co/YBQkYhfZno

@atypical_me @olijrobinson @Muireann_Irish @DanielaJPalombo @danjlurie @waterlego @StuartJRitchie @SimonRCox @Don_lyall @rogierK @Aman_Badhwar The top-down figures were done in ParaView, mostly following procedures described here (https://t.co/r2Qh8D3JMa);

@DrMowinckels No problem! I think this is less relevant, but may also be useful https://t.co/r2Qh8D3JMa

@c_perrodin I could send you the STL of the 3D model I used in Fig 5 here (https://t.co/r2Qh8D3JMa)

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

RT @cMadan: For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa…

For the curious, this is the paper being cited: Creating 3D visualizations of MRI data: A brief guide https://t.co/r2Qh8D3JMa https://t.co/Prh1AUZoKA

@caitvw from existing figs, only one that comes to mind is this one https://t.co/K9ghHqR3Kq

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

RT @HippocampusCam: Results from a Neurosynth search for "default mode" (516 studies). Visualization generated using @cMadan's pipeline: ht…

@vaughanbell with some tinkering, see https://t.co/dPbI8LteOR

@SciMeg @MachinaCorp @UAlberta ooh, (human) hippocampus is my favorite region, but... https://t.co/K9ghHqR3Kq

@realscientists if you have MRIs to start with, this might help with the 3D viz part: https://t.co/dPbI8LteOR

Comparative neuroanatomy of whole-brain and hippocampal brain volumes. via @cMadan https://t.co/2zzyP2dU45 https://t.co/CEkrtESF1U

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

@satra_ @EvoMRI @R3RT0 @katjaQheuer @amyleerobinson traced volumes can easily be converted to meshes with ITK-SNAP, https://t.co/wqDPEheeHW

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

RT @cMadan: Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjo…

@R3RT0 too bad I can't see the site now! I only work with human MRIs, but fun to work with others, see Fig 5 here https://t.co/KR2WeDeJwx

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @Neuro_Skeptic: Creating 3D visualizations of MRI data: a brief guide https://t.co/AhFPYM7jW2 Beyond plotting blobs on slices. By @cMadan

RT @m_wall: Really great guide to creating beautiful 3D brain visualisations, using ITK-Snap and Paraview, by @cMadan http://t.co/w3OKlZ9j…

Great guide for making dem purdy 3D brain pictures http://t.co/P8lDTm8EVW @cMadan

RT @m_wall: Really great guide to creating beautiful 3D brain visualisations, using ITK-Snap and Paraview, by @cMadan http://t.co/w3OKlZ9j…

RT @m_wall: Really great guide to creating beautiful 3D brain visualisations, using ITK-Snap and Paraview, by @cMadan http://t.co/w3OKlZ9j…

Really great guide to creating beautiful 3D brain visualisations, using ITK-Snap and Paraview, by @cMadan http://t.co/w3OKlZ9jGv

RT @ChrisFiloG: Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

RT @ChrisFiloG: Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

RT @ChrisFiloG: Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

RT @ChrisFiloG: Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

RT @ChrisFiloG: Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

RT @ChrisFiloG: Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

Creating 3D visualizations of MRI data: A brief guide. Madan CR, published by @F1000Research, http://t.co/PqcGpZr6cr

RT @Helena_LB: Where you can, for example, find @cMadan's latest paper (reviewed by @fMRI_guy & @wandedob): http://t.co/umpDZZaE2Y https://…

Where you can, for example, find @cMadan's latest paper (reviewed by @fMRI_guy & @wandedob): http://t.co/umpDZZaE2Y https://t.co/ye93PNlHDZ

Want to make 3D figures of MRI data like these? Take a look at my brief guide! http://t.co/KR2WeDeJwx http://t.co/ozkdOU4sPN

Want to make 3D figures of MRI data like these? Take a look at my brief guide! http://t.co/KR2WeDeJwx http://t.co/ozkdOU4sPN

Want to make 3D figures of MRI data like these? Take a look at my brief guide! http://t.co/KR2WeDeJwx http://t.co/ozkdOU4sPN

Want to make 3D figures of MRI data like these? Take a look at my brief guide! http://t.co/KR2WeDeJwx http://t.co/ozkdOU4sPN

Awhile back I was asking about MRI atlases of animals, here's what I made. Details in http://t.co/KR2WeDeJwx http://t.co/ceRAjoRFzh