From elef at indiana.edu  Wed May  1 13:27:52 2019
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Wed, 1 May 2019 13:27:52 -0400
Subject: [Neuroimaging] ANN: DIPY 0.16.0 release
Message-ID: <CAN6JmWNA1C=7A928ZT1obGntPtngooG2wW95upR3V3DjekwLoA@mail.gmail.com>

Hello all!,


We are excited to announce a new release of Diffusion Imaging in Python
(DIPY).

If you use DIPY in your research, please cite us using the following
DOI: 10.3389/fninf.2014.00008
<https://www.ncbi.nlm.nih.gov/pubmed/24600385>

DIPY 0.16 (Monday, 10 March 2019)

This release received contributions from 14 developers (the full release
notes are at: http://dipy.org/release0.16.html
<http://nipy.org/dipy/release0.16.html>). Thank you for your contributions
and feedback!

Highlights of this release include:

   -

   Horizon, medical visualization interface powered by QuickBundlesX.
   -

   New Tractometry tools: Bundle Analysis / Bundle Profiles.
   -

   New reconstruction model: IVIM MIX (Variable Projection).
   -

   New command line interface: Affine and Diffeomorphic Registration.
   -

   New command line interface: Probabilistic, Deterministic and PFT
   Tracking.
   -

   Integration of Cython Guidelines for developers.
   -

   Replacement of Nose by Pytest.
   -

   Documentation update.
   -

   Closed 103 issues and merged 41 pull requests.

Note:

   -

   DIPY 0.16.0 will be the last version to support Python 2. The next
   release, DIPY 1.0.0,  will support Python 3 only.



To upgrade or install <http://dipy.org/release0.10.html> DIPY

Run the following command in your terminal:
<http://dipy.org/release0.10.html>

pip install --upgrade dipy

or

conda install -c conda-forge dipy

This version of DIPY depends on nibabel (2.3.0+).

Questions or suggestions?

For any questions go to http://dipy.org, or send an e-mail to
dipy at python.org <neuroimaging at python.org>

We also have an instant messaging service and chat room available at
https://gitter.im/nipy/dipy

On behalf of the DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

http://dipy.org/developers.html
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From j.schreiber at fz-juelich.de  Thu May  2 08:36:59 2019
From: j.schreiber at fz-juelich.de (Jan Schreiber)
Date: Thu, 2 May 2019 14:36:59 +0200
Subject: [Neuroimaging] ANN: DIPY 0.16.0 release
In-Reply-To: <CAN6JmWNA1C=7A928ZT1obGntPtngooG2wW95upR3V3DjekwLoA@mail.gmail.com>
References: <CAN6JmWNA1C=7A928ZT1obGntPtngooG2wW95upR3V3DjekwLoA@mail.gmail.com>
Message-ID: <cdc27d3c-d6a5-dda3-f025-8020ccd7a792@fz-juelich.de>

Dear Dipy Developers,

Congratulations and thank you so much for this great library! :+1:
The highlight are looking very exciting :-)

Best,
Jan



On 5/1/19 7:27 PM, Eleftherios Garyfallidis wrote:
> Hello all!,
>
>
> We are excited to announce a new release of Diffusion Imaging in Python
> (DIPY).
>
>
> If you use DIPY in your research, please cite us using the following
> DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385>
>
>
> DIPY 0.16 (Monday, 10 March 2019)
>
> This release received contributions from 14 developers (the full release
> notes are at: http://dipy.org/release0.16.html
> <http://nipy.org/dipy/release0.16.html>). Thank you for your
> contributions and feedback!
>
>
> Highlights of this release include:
>
>   *
>
>     Horizon, medical visualization interface powered by QuickBundlesX.
>
>   *
>
>     New Tractometry tools: Bundle Analysis / Bundle Profiles.
>
>   *
>
>     New reconstruction model: IVIM MIX (Variable Projection).
>
>   *
>
>     New command line interface: Affine and Diffeomorphic Registration.
>
>   *
>
>     New command line interface: Probabilistic, Deterministic and PFT
>     Tracking.
>
>   *
>
>     Integration of Cython Guidelines for developers.
>
>   *
>
>     Replacement of Nose by Pytest.
>
>   *
>
>     Documentation update.
>
>   *
>
>     Closed 103 issues and merged 41 pull requests.
>
> Note:
>
>   *
>
>     DIPY 0.16.0 will be the last version to support Python 2. The next
>     release, DIPY 1.0.0,  will support Python 3 only.
>
>
>
> To upgrade or install <http://dipy.org/release0.10.html>DIPY
>
>
> Run the following command in your terminal:
> <http://dipy.org/release0.10.html>
>
>
> pip install --upgrade dipy
>
>
> or
>
>
> conda install -c conda-forge dipy
>
>
> This version of DIPY depends on nibabel (2.3.0+).
>
>
> Questions or suggestions?
>
> For any questions go to http://dipy.org <http://dipy.org/>, or send an
> e-mail to dipy at python.org <mailto:neuroimaging at python.org>
>
> We also have an instant messaging service and chat room available at
> https://gitter.im/nipy/dipy
>
>
> On behalf of the DIPY developers,
>
> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>
> http://dipy.org/developers.html
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>


------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------


From marvin.albert at gmail.com  Sun May 19 13:52:38 2019
From: marvin.albert at gmail.com (Marvin Albert)
Date: Sun, 19 May 2019 19:52:38 +0200
Subject: [Neuroimaging] SyN registration: Weird effect when updating
 sigma_diff between resolution levels
Message-ID: <28B82003-E5B5-40F6-BE6F-51499E3E4563@gmail.com>

Hi,

first of all thanks a lot for the great open source tools, I?m using dipy?s image registration extensively.

I have a question regarding using SymmetricDiffeomorphicRegistration in combination with CCMetric.

I?m optimising the registration performance for my application (zebrafish embryos imaged with fluorescence microscopy). More specifically, I am playing around with the scaling factors of the scale space and the update field smoothing (parameter sigma_diff in CCMetric). To do so, I modified the registration process in such a way that I can manually set the current scaling factor and sigma_diff (taking advantage of the fact that dipy is written in accessible python!). 

I found parameter sets which achieve significantly better performance for my dataset than the presets (meaning doubling of scaling factors in each level and constant sigma_diff). So far so good.

However, there?s an odd behaviour I don't understand. Often when I decrease sigma_diff from one level to the next, the metric increases instead of decreasing. However, when I run the two levels with different sigma_diffs in separate registration calls, the metric nicely decreases as expected and registration performance improves. Why is this and is this supposed to happen?

I tried to come up with a minimal example shown in this jupiter notebook: https://github.com/quakberto/dipy_syn/blob/master/test_syn_sigma_diffs.ipynb <https://github.com/quakberto/dipy_syn/blob/master/test_syn_sigma_diffs.ipynb>. The notebook also shows the custom code I use for creating the modified scale space.

Here?s a short summary:
- I generate a random static image S and rotate it to get a moving image M
- I run registrations with different sigma_diffs:
  - a) one level, constant sigma_diff = 1 (S,M)->M_a
  - b) one level, constant sigma_diff = 2 (S,M)->M_b
  - c) two levels, decreasing sigma_diffs = [2,1] (S,M)->M_c
  - d) one level, sigma_diff = 1, starting with M_b: (S,M_b)->M_c

Now, using the normalised cross correlation and also the sum of norms of differences between the experimental and ground truth displacement fields as metrics, surprisingly case c) performs worse than b). However, case d) greatly improves on the outcome of b). Here's a figure:



My question is: Why does the last level in case c) deteriorate the registration performance? And why does a fresh run behave so differently?

It got a bit lengthy so thanks a lot if you?re still reading! I?m happy for any comments.

Best,
Marvin


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From alexandre.gramfort at inria.fr  Tue May 21 15:34:53 2019
From: alexandre.gramfort at inria.fr (Alexandre Gramfort)
Date: Tue, 21 May 2019 21:34:53 +0200
Subject: [Neuroimaging] [ANN] MNE-Python 0.18
Message-ID: <CADeotZoLT-jTZ0iMW36p8k8koFJLvZ3+PG87w7hD7xu7+oBPHQ@mail.gmail.com>

Dear community!

We are very pleased to announce the new 0.18 release of MNE-Python
(http://martinos.org/mne/stable/).

A few highlights
================

- Python 2 is no longer supported; MNE-Python now requires Python 3.5+
- New tutorials and examples on sleep stage classification, data
simulation using subject's anatomy, how to use EEG montages on
fsaverage
- New module to simulate SourceEstimates
- Improved performance using CUDA, better copy management, better
dispatching of the computation over the channels
- New fetchers for polysomnography (PSG) recordings from Physionet and
fsaverage template
- Better support for source reconstruction with beamformers and other
inverse models
- Improved UI and visualizations for topomaps, Raw and Epochs objects
- Better support for Annotations
- Support to compute power envelope correlations on brain parcellation
for rest data
- Better rendering of the coregistration
- Added partial support for PyVista as a 3D backend that can replace mayavi
- Added support for Raw, Epochs and Evoked noise simulation
- Added new parcellation (448-labels subdivided aparc) and improve
support including morphing of the labels
- Better support for the TFR objects

And we caught and fixed more than 50 bugs!

Notable API changes
===================

- Deprecation of `mne.realtime` module to become entire project in the
MNE echosystem
- Deprecation of `mne.io.find_edf_events`, `raw.estimate_rank`
- Reading BDF and GDF files with `mne.io.read_raw_edf` is deprecated
and replaced by `mne.io.read_raw_bdf` and `mne.io.read_raw_gdf`
- The signatures of `mne.preprocessing.ICA`,
`mne.simulation.add_noise` and `mne.simulation.add_chpi` have changed
- Added overwrite parameter in `mne.Epochs.save`
- `mne.minimum_norm.apply_inverse` now returns
`mne.VolVectorSourceEstimate` when needed
- Annotations are now kept sorted by onset
- `peak_finder` should be imported as: `from mne.preprocessing import
peak_finder`


For a full list of improvements and API changes see:
http://martinos.org/mne/stable/whats_new.html#version-0-18

To install the latest release the following command should do the job:

    $ pip install --upgrade mne

As usual, we welcome your bug reports, feature requests, critiques,
and contributions.

Some links:
- https://github.com/mne-tools/mne-python (code + readme on how to install)
- http://martinos.org/mne/stable/ (full MNE documentation)

Follow us on Twitter for general news (https://twitter.com/mne_news)
and for a regular feed of merged PRs (https://twitter.com/mne_python).

Regards,
The MNE-Python developers

52 people made commits that contributed to this release (in alphabetical order):

* Achilleas Koutsou
* Alexander Kovrig
* Alexandre Gramfort
* Antoine Gauthier
* Britta Westner
* Bruno Nicenboim
* Burkhard Maess
* Chris Bailey
* Chris Holdgraf
* Christian Brodbeck
* Clemens Brunner
* Crist?bal Mo?nne-Loccoz
* Daniel McCloy
* David Haslacher
* Denis A. Engemann
* Dirk G?tlin
* Eric Larson
* Evgenii Kalenkovich
* Fede Raimondo
* Guillaume Favelier
* Hubert Banville
* Ivana Kojcic
* Jean-Remi King
* Jeff Hanna
* Joan Massich
* Johannes Kasper
* Jon Houck
* Jona Sassenhagen
* Jos? C. Garc?a Alanis
* Jussi Nurminen
* Katarina Slama
* Keith Doelling
* Kostiantyn Maksymenko
* Larry Eisenman
* Legrand Nicolas
* Mainak Jas
* Marijn van Vliet
* Mikolaj Magnuski
* Nathalie Gayraud
* Nikolas Chalas
* Oleh Kozynets
* Quentin Bertrand
* Samuel Deslauriers-Gauthier
* Sebasti?n Casta?o
* Simon Kern
* Stanislas Chambon
* Stefan Appelhoff
* Stefan Repplinger
* Steve Matindi
* Teon Brooks
* Thomas Donoghue
* Thomas Hartmann

From bertrand.thirion at inria.fr  Tue May 21 15:41:37 2019
From: bertrand.thirion at inria.fr (Bertrand Thirion)
Date: Tue, 21 May 2019 21:41:37 +0200 (CEST)
Subject: [Neuroimaging] [ANN] MNE-Python 0.18
In-Reply-To: <CADeotZoLT-jTZ0iMW36p8k8koFJLvZ3+PG87w7hD7xu7+oBPHQ@mail.gmail.com>
References: <CADeotZoLT-jTZ0iMW36p8k8koFJLvZ3+PG87w7hD7xu7+oBPHQ@mail.gmail.com>
Message-ID: <730352127.8118829.1558467697458.JavaMail.zimbra@inria.fr>

Congratulations ! 
B

----- Mail original -----
> De: "Alexandre Gramfort" <alexandre.gramfort at inria.fr>
> ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>, megcommunity at jiscmail.ac.uk
> Envoy?: Mardi 21 Mai 2019 21:34:53
> Objet: [Neuroimaging] [ANN] MNE-Python 0.18

> Dear community!
> 
> We are very pleased to announce the new 0.18 release of MNE-Python
> (http://martinos.org/mne/stable/).
> 
> A few highlights
> ================
> 
> - Python 2 is no longer supported; MNE-Python now requires Python 3.5+
> - New tutorials and examples on sleep stage classification, data
> simulation using subject's anatomy, how to use EEG montages on
> fsaverage
> - New module to simulate SourceEstimates
> - Improved performance using CUDA, better copy management, better
> dispatching of the computation over the channels
> - New fetchers for polysomnography (PSG) recordings from Physionet and
> fsaverage template
> - Better support for source reconstruction with beamformers and other
> inverse models
> - Improved UI and visualizations for topomaps, Raw and Epochs objects
> - Better support for Annotations
> - Support to compute power envelope correlations on brain parcellation
> for rest data
> - Better rendering of the coregistration
> - Added partial support for PyVista as a 3D backend that can replace mayavi
> - Added support for Raw, Epochs and Evoked noise simulation
> - Added new parcellation (448-labels subdivided aparc) and improve
> support including morphing of the labels
> - Better support for the TFR objects
> 
> And we caught and fixed more than 50 bugs!
> 
> Notable API changes
> ===================
> 
> - Deprecation of `mne.realtime` module to become entire project in the
> MNE echosystem
> - Deprecation of `mne.io.find_edf_events`, `raw.estimate_rank`
> - Reading BDF and GDF files with `mne.io.read_raw_edf` is deprecated
> and replaced by `mne.io.read_raw_bdf` and `mne.io.read_raw_gdf`
> - The signatures of `mne.preprocessing.ICA`,
> `mne.simulation.add_noise` and `mne.simulation.add_chpi` have changed
> - Added overwrite parameter in `mne.Epochs.save`
> - `mne.minimum_norm.apply_inverse` now returns
> `mne.VolVectorSourceEstimate` when needed
> - Annotations are now kept sorted by onset
> - `peak_finder` should be imported as: `from mne.preprocessing import
> peak_finder`
> 
> 
> For a full list of improvements and API changes see:
> http://martinos.org/mne/stable/whats_new.html#version-0-18
> 
> To install the latest release the following command should do the job:
> 
>    $ pip install --upgrade mne
> 
> As usual, we welcome your bug reports, feature requests, critiques,
> and contributions.
> 
> Some links:
> - https://github.com/mne-tools/mne-python (code + readme on how to install)
> - http://martinos.org/mne/stable/ (full MNE documentation)
> 
> Follow us on Twitter for general news (https://twitter.com/mne_news)
> and for a regular feed of merged PRs (https://twitter.com/mne_python).
> 
> Regards,
> The MNE-Python developers
> 
> 52 people made commits that contributed to this release (in alphabetical order):
> 
> * Achilleas Koutsou
> * Alexander Kovrig
> * Alexandre Gramfort
> * Antoine Gauthier
> * Britta Westner
> * Bruno Nicenboim
> * Burkhard Maess
> * Chris Bailey
> * Chris Holdgraf
> * Christian Brodbeck
> * Clemens Brunner
> * Crist?bal Mo?nne-Loccoz
> * Daniel McCloy
> * David Haslacher
> * Denis A. Engemann
> * Dirk G?tlin
> * Eric Larson
> * Evgenii Kalenkovich
> * Fede Raimondo
> * Guillaume Favelier
> * Hubert Banville
> * Ivana Kojcic
> * Jean-Remi King
> * Jeff Hanna
> * Joan Massich
> * Johannes Kasper
> * Jon Houck
> * Jona Sassenhagen
> * Jos? C. Garc?a Alanis
> * Jussi Nurminen
> * Katarina Slama
> * Keith Doelling
> * Kostiantyn Maksymenko
> * Larry Eisenman
> * Legrand Nicolas
> * Mainak Jas
> * Marijn van Vliet
> * Mikolaj Magnuski
> * Nathalie Gayraud
> * Nikolas Chalas
> * Oleh Kozynets
> * Quentin Bertrand
> * Samuel Deslauriers-Gauthier
> * Sebasti?n Casta?o
> * Simon Kern
> * Stanislas Chambon
> * Stefan Appelhoff
> * Stefan Repplinger
> * Steve Matindi
> * Teon Brooks
> * Thomas Donoghue
> * Thomas Hartmann
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From satra at mit.edu  Tue May 21 16:53:29 2019
From: satra at mit.edu (Satrajit Ghosh)
Date: Tue, 21 May 2019 16:53:29 -0400
Subject: [Neuroimaging] [ANN] MNE-Python 0.18
In-Reply-To: <730352127.8118829.1558467697458.JavaMail.zimbra@inria.fr>
References: <CADeotZoLT-jTZ0iMW36p8k8koFJLvZ3+PG87w7hD7xu7+oBPHQ@mail.gmail.com>
 <730352127.8118829.1558467697458.JavaMail.zimbra@inria.fr>
Message-ID: <CA+A4wOk_KrszkFn-fYVjwCd8xtzSpXbaPctDDvx8BJbat8XL_w@mail.gmail.com>

keep up the great work!

cheers,

satra

On Tue, May 21, 2019 at 3:45 PM Bertrand Thirion <bertrand.thirion at inria.fr>
wrote:

> Congratulations !
> B
>
> ----- Mail original -----
> > De: "Alexandre Gramfort" <alexandre.gramfort at inria.fr>
> > ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>,
> megcommunity at jiscmail.ac.uk
> > Envoy?: Mardi 21 Mai 2019 21:34:53
> > Objet: [Neuroimaging] [ANN] MNE-Python 0.18
>
> > Dear community!
> >
> > We are very pleased to announce the new 0.18 release of MNE-Python
> > (http://martinos.org/mne/stable/).
> >
> > A few highlights
> > ================
> >
> > - Python 2 is no longer supported; MNE-Python now requires Python 3.5+
> > - New tutorials and examples on sleep stage classification, data
> > simulation using subject's anatomy, how to use EEG montages on
> > fsaverage
> > - New module to simulate SourceEstimates
> > - Improved performance using CUDA, better copy management, better
> > dispatching of the computation over the channels
> > - New fetchers for polysomnography (PSG) recordings from Physionet and
> > fsaverage template
> > - Better support for source reconstruction with beamformers and other
> > inverse models
> > - Improved UI and visualizations for topomaps, Raw and Epochs objects
> > - Better support for Annotations
> > - Support to compute power envelope correlations on brain parcellation
> > for rest data
> > - Better rendering of the coregistration
> > - Added partial support for PyVista as a 3D backend that can replace
> mayavi
> > - Added support for Raw, Epochs and Evoked noise simulation
> > - Added new parcellation (448-labels subdivided aparc) and improve
> > support including morphing of the labels
> > - Better support for the TFR objects
> >
> > And we caught and fixed more than 50 bugs!
> >
> > Notable API changes
> > ===================
> >
> > - Deprecation of `mne.realtime` module to become entire project in the
> > MNE echosystem
> > - Deprecation of `mne.io.find_edf_events`, `raw.estimate_rank`
> > - Reading BDF and GDF files with `mne.io.read_raw_edf` is deprecated
> > and replaced by `mne.io.read_raw_bdf` and `mne.io.read_raw_gdf`
> > - The signatures of `mne.preprocessing.ICA`,
> > `mne.simulation.add_noise` and `mne.simulation.add_chpi` have changed
> > - Added overwrite parameter in `mne.Epochs.save`
> > - `mne.minimum_norm.apply_inverse` now returns
> > `mne.VolVectorSourceEstimate` when needed
> > - Annotations are now kept sorted by onset
> > - `peak_finder` should be imported as: `from mne.preprocessing import
> > peak_finder`
> >
> >
> > For a full list of improvements and API changes see:
> > http://martinos.org/mne/stable/whats_new.html#version-0-18
> >
> > To install the latest release the following command should do the job:
> >
> >    $ pip install --upgrade mne
> >
> > As usual, we welcome your bug reports, feature requests, critiques,
> > and contributions.
> >
> > Some links:
> > - https://github.com/mne-tools/mne-python (code + readme on how to
> install)
> > - http://martinos.org/mne/stable/ (full MNE documentation)
> >
> > Follow us on Twitter for general news (https://twitter.com/mne_news)
> > and for a regular feed of merged PRs (https://twitter.com/mne_python).
> >
> > Regards,
> > The MNE-Python developers
> >
> > 52 people made commits that contributed to this release (in alphabetical
> order):
> >
> > * Achilleas Koutsou
> > * Alexander Kovrig
> > * Alexandre Gramfort
> > * Antoine Gauthier
> > * Britta Westner
> > * Bruno Nicenboim
> > * Burkhard Maess
> > * Chris Bailey
> > * Chris Holdgraf
> > * Christian Brodbeck
> > * Clemens Brunner
> > * Crist?bal Mo?nne-Loccoz
> > * Daniel McCloy
> > * David Haslacher
> > * Denis A. Engemann
> > * Dirk G?tlin
> > * Eric Larson
> > * Evgenii Kalenkovich
> > * Fede Raimondo
> > * Guillaume Favelier
> > * Hubert Banville
> > * Ivana Kojcic
> > * Jean-Remi King
> > * Jeff Hanna
> > * Joan Massich
> > * Johannes Kasper
> > * Jon Houck
> > * Jona Sassenhagen
> > * Jos? C. Garc?a Alanis
> > * Jussi Nurminen
> > * Katarina Slama
> > * Keith Doelling
> > * Kostiantyn Maksymenko
> > * Larry Eisenman
> > * Legrand Nicolas
> > * Mainak Jas
> > * Marijn van Vliet
> > * Mikolaj Magnuski
> > * Nathalie Gayraud
> > * Nikolas Chalas
> > * Oleh Kozynets
> > * Quentin Bertrand
> > * Samuel Deslauriers-Gauthier
> > * Sebasti?n Casta?o
> > * Simon Kern
> > * Stanislas Chambon
> > * Stefan Appelhoff
> > * Stefan Repplinger
> > * Steve Matindi
> > * Teon Brooks
> > * Thomas Donoghue
> > * Thomas Hartmann
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From jbpoline at gmail.com  Tue May 21 17:22:26 2019
From: jbpoline at gmail.com (JB Poline)
Date: Tue, 21 May 2019 17:22:26 -0400
Subject: [Neuroimaging] [ANN] MNE-Python 0.18
In-Reply-To: <CA+A4wOk_KrszkFn-fYVjwCd8xtzSpXbaPctDDvx8BJbat8XL_w@mail.gmail.com>
References: <CADeotZoLT-jTZ0iMW36p8k8koFJLvZ3+PG87w7hD7xu7+oBPHQ@mail.gmail.com>
 <730352127.8118829.1558467697458.JavaMail.zimbra@inria.fr>
 <CA+A4wOk_KrszkFn-fYVjwCd8xtzSpXbaPctDDvx8BJbat8XL_w@mail.gmail.com>
Message-ID: <CALMaa80G3rfZ0HYY=wXH1wXZfo7XoQ5ZB9p89FeimS3mrH+85g@mail.gmail.com>

Congrats !
JB

On Tue, May 21, 2019 at 4:59 PM Satrajit Ghosh <satra at mit.edu> wrote:

> keep up the great work!
>
> cheers,
>
> satra
>
> On Tue, May 21, 2019 at 3:45 PM Bertrand Thirion <
> bertrand.thirion at inria.fr> wrote:
>
>> Congratulations !
>> B
>>
>> ----- Mail original -----
>> > De: "Alexandre Gramfort" <alexandre.gramfort at inria.fr>
>> > ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>,
>> megcommunity at jiscmail.ac.uk
>> > Envoy?: Mardi 21 Mai 2019 21:34:53
>> > Objet: [Neuroimaging] [ANN] MNE-Python 0.18
>>
>> > Dear community!
>> >
>> > We are very pleased to announce the new 0.18 release of MNE-Python
>> > (http://martinos.org/mne/stable/).
>> >
>> > A few highlights
>> > ================
>> >
>> > - Python 2 is no longer supported; MNE-Python now requires Python 3.5+
>> > - New tutorials and examples on sleep stage classification, data
>> > simulation using subject's anatomy, how to use EEG montages on
>> > fsaverage
>> > - New module to simulate SourceEstimates
>> > - Improved performance using CUDA, better copy management, better
>> > dispatching of the computation over the channels
>> > - New fetchers for polysomnography (PSG) recordings from Physionet and
>> > fsaverage template
>> > - Better support for source reconstruction with beamformers and other
>> > inverse models
>> > - Improved UI and visualizations for topomaps, Raw and Epochs objects
>> > - Better support for Annotations
>> > - Support to compute power envelope correlations on brain parcellation
>> > for rest data
>> > - Better rendering of the coregistration
>> > - Added partial support for PyVista as a 3D backend that can replace
>> mayavi
>> > - Added support for Raw, Epochs and Evoked noise simulation
>> > - Added new parcellation (448-labels subdivided aparc) and improve
>> > support including morphing of the labels
>> > - Better support for the TFR objects
>> >
>> > And we caught and fixed more than 50 bugs!
>> >
>> > Notable API changes
>> > ===================
>> >
>> > - Deprecation of `mne.realtime` module to become entire project in the
>> > MNE echosystem
>> > - Deprecation of `mne.io.find_edf_events`, `raw.estimate_rank`
>> > - Reading BDF and GDF files with `mne.io.read_raw_edf` is deprecated
>> > and replaced by `mne.io.read_raw_bdf` and `mne.io.read_raw_gdf`
>> > - The signatures of `mne.preprocessing.ICA`,
>> > `mne.simulation.add_noise` and `mne.simulation.add_chpi` have changed
>> > - Added overwrite parameter in `mne.Epochs.save`
>> > - `mne.minimum_norm.apply_inverse` now returns
>> > `mne.VolVectorSourceEstimate` when needed
>> > - Annotations are now kept sorted by onset
>> > - `peak_finder` should be imported as: `from mne.preprocessing import
>> > peak_finder`
>> >
>> >
>> > For a full list of improvements and API changes see:
>> > http://martinos.org/mne/stable/whats_new.html#version-0-18
>> >
>> > To install the latest release the following command should do the job:
>> >
>> >    $ pip install --upgrade mne
>> >
>> > As usual, we welcome your bug reports, feature requests, critiques,
>> > and contributions.
>> >
>> > Some links:
>> > - https://github.com/mne-tools/mne-python (code + readme on how to
>> install)
>> > - http://martinos.org/mne/stable/ (full MNE documentation)
>> >
>> > Follow us on Twitter for general news (https://twitter.com/mne_news)
>> > and for a regular feed of merged PRs (https://twitter.com/mne_python).
>> >
>> > Regards,
>> > The MNE-Python developers
>> >
>> > 52 people made commits that contributed to this release (in
>> alphabetical order):
>> >
>> > * Achilleas Koutsou
>> > * Alexander Kovrig
>> > * Alexandre Gramfort
>> > * Antoine Gauthier
>> > * Britta Westner
>> > * Bruno Nicenboim
>> > * Burkhard Maess
>> > * Chris Bailey
>> > * Chris Holdgraf
>> > * Christian Brodbeck
>> > * Clemens Brunner
>> > * Crist?bal Mo?nne-Loccoz
>> > * Daniel McCloy
>> > * David Haslacher
>> > * Denis A. Engemann
>> > * Dirk G?tlin
>> > * Eric Larson
>> > * Evgenii Kalenkovich
>> > * Fede Raimondo
>> > * Guillaume Favelier
>> > * Hubert Banville
>> > * Ivana Kojcic
>> > * Jean-Remi King
>> > * Jeff Hanna
>> > * Joan Massich
>> > * Johannes Kasper
>> > * Jon Houck
>> > * Jona Sassenhagen
>> > * Jos? C. Garc?a Alanis
>> > * Jussi Nurminen
>> > * Katarina Slama
>> > * Keith Doelling
>> > * Kostiantyn Maksymenko
>> > * Larry Eisenman
>> > * Legrand Nicolas
>> > * Mainak Jas
>> > * Marijn van Vliet
>> > * Mikolaj Magnuski
>> > * Nathalie Gayraud
>> > * Nikolas Chalas
>> > * Oleh Kozynets
>> > * Quentin Bertrand
>> > * Samuel Deslauriers-Gauthier
>> > * Sebasti?n Casta?o
>> > * Simon Kern
>> > * Stanislas Chambon
>> > * Stefan Appelhoff
>> > * Stefan Repplinger
>> > * Steve Matindi
>> > * Teon Brooks
>> > * Thomas Donoghue
>> > * Thomas Hartmann
>> > _______________________________________________
>> > Neuroimaging mailing list
>> > Neuroimaging at python.org
>> > https://mail.python.org/mailman/listinfo/neuroimaging
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From hesnaezgi at gmail.com  Sat May 25 19:38:42 2019
From: hesnaezgi at gmail.com (=?UTF-8?Q?Hesna_Ezgi_A=C5=9EKIN?=)
Date: Sun, 26 May 2019 02:38:42 +0300
Subject: [Neuroimaging] Python for fMRI
Message-ID: <CAFOyzKzHtNRYPZ7nwM-hYMM=sJUW-bpeZDYqyCNa3cNLASMb4A@mail.gmail.com>

Hello,

I'm a molecular biology and genetics student trying to learn coding with
Python. I have figured out that I should use couple of libraries and
managed to visualize the fMRI data coming in the format ".nii" as a brain
image in Python. Now I'm trying to create a kind of heatmap, but I cannot
imagine a way to basically sum up the matrices in .nii format in different
folders (for different patients), or should I use some package like Seaborn?

There might be a couple of ways, I just wanted to know the most suitable
method for fMRI, and couldn't find someone around me who is knowledgable
about both Python and fMRI.

Thanks in advance. Regards,

Hesna Ezgi
+905416799793
Bogazici University, 34470
Bebek / Istanbul / Turkey
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From bennet at umich.edu  Mon May 27 08:33:36 2019
From: bennet at umich.edu (Bennet Fauber)
Date: Mon, 27 May 2019 08:33:36 -0400
Subject: [Neuroimaging] Python for fMRI
In-Reply-To: <CAFOyzKzHtNRYPZ7nwM-hYMM=sJUW-bpeZDYqyCNa3cNLASMb4A@mail.gmail.com>
References: <CAFOyzKzHtNRYPZ7nwM-hYMM=sJUW-bpeZDYqyCNa3cNLASMb4A@mail.gmail.com>
Message-ID: <CAB2ovosvBA8tp7ORqiKmLQ5VBQvoA8pGUZqEVcqujZOHUcQiCw@mail.gmail.com>

You might find something in the documentation for Nibabel at

    https://nipy.org/nibabel/coordinate_systems.html#voxel-coordinates-are-in-voxel-space

There is an example there of displaying the brain using a grey-scale
'heatmap', I think.  You might find what you want by changing the
cmap="gray" to something else.

You might also want to look at

    https://bic-berkeley.github.io/psych-214-fall-2016/index.html

which was a course devoted to Python and brain imaging analysis.

Both of those were useful to me.


On Mon, May 27, 2019 at 8:02 AM Hesna Ezgi A?KIN <hesnaezgi at gmail.com> wrote:
>
> Hello,
>
> I'm a molecular biology and genetics student trying to learn coding with Python. I have figured out that I should use couple of libraries and managed to visualize the fMRI data coming in the format ".nii" as a brain image in Python. Now I'm trying to create a kind of heatmap, but I cannot imagine a way to basically sum up the matrices in .nii format in different folders (for different patients), or should I use some package like Seaborn?
>
> There might be a couple of ways, I just wanted to know the most suitable method for fMRI, and couldn't find someone around me who is knowledgable about both Python and fMRI.
>
> Thanks in advance. Regards,
>
> Hesna Ezgi
> +905416799793
> Bogazici University, 34470
> Bebek / Istanbul / Turkey
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From christophe at pallier.org  Mon May 27 08:36:26 2019
From: christophe at pallier.org (Christophe Pallier)
Date: Mon, 27 May 2019 14:36:26 +0200
Subject: [Neuroimaging] Python for fMRI
In-Reply-To: <CAFOyzKzHtNRYPZ7nwM-hYMM=sJUW-bpeZDYqyCNa3cNLASMb4A@mail.gmail.com>
References: <CAFOyzKzHtNRYPZ7nwM-hYMM=sJUW-bpeZDYqyCNa3cNLASMb4A@mail.gmail.com>
Message-ID: <CALyk9bwNLzvRdnkTUa8oXbBQB+yfSoX571tOnMOg+=OZKUZR0w@mail.gmail.com>

Hi,

You did not specify what kind of images your are manipulating and what
exactly you want to do.
But, say you want to display the average from a set of images*, you could
do:


    import glob
    import nilearn

    images = glob.glob('*/*.nii')
    avg = nilearn.image.mean_img(images)

and then use one of the nilearn.plotting functions to display `avg`.


On Mon, May 27, 2019 at 2:02 PM Hesna Ezgi A?KIN <hesnaezgi at gmail.com>
wrote:

> Hello,
>
> I'm a molecular biology and genetics student trying to learn coding with
> Python. I have figured out that I should use couple of libraries and
> managed to visualize the fMRI data coming in the format ".nii" as a brain
> image in Python. Now I'm trying to create a kind of heatmap, but I cannot
> imagine a way to basically sum up the matrices in .nii format in different
> folders (for different patients), or should I use some package like Seaborn?
>
> There might be a couple of ways, I just wanted to know the most suitable
> method for fMRI, and couldn't find someone around me who is knowledgable
> about both Python and fMRI.
>
> Thanks in advance. Regards,
>
> Hesna Ezgi
> +905416799793
> Bogazici University, 34470
> Bebek / Istanbul / Turkey
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>


-- 
--
Christophe Pallier <christophe at pallier.org>
INSERM-CEA Cognitive Neuroimaging Lab, Neurospin, bat 145,
91191 Gif-sur-Yvette Cedex, France
Tel: 00 33 1 69 08 79 34
Personal web site: http://www.pallier.org
Lab web site: http://www.unicog.org
https://www.chronicle.com/interactives/is-email-making-professors-stupid?
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From markiewicz at stanford.edu  Tue May 28 10:09:57 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Tue, 28 May 2019 14:09:57 +0000
Subject: [Neuroimaging] ANN: nibabel 2.4.1
Message-ID: <BN6PR02MB26751349B6E2B528FD6388ADA91E0@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi all,

Just a quick announcement that nibabel has a new bug-fix release, version 2.4.1. The next anticipated release will be 2.5.0, targeted for July, and 2.5.x will be the last of the Python 2-compatible series, with bug-fix-only support through the *end* of 2020.

Probably the highest-impact change in 2.4.1 is that all DataobjImages accept the `mmap` keyword argument on a best-effort basis, so `nibabel.load(fname, mmap=False)` will now succeed for all but GIFTI images. Additionally, GIFTI data arrays are editable again with recent numpy, and FreeSurfer annotation files can be written more reliably.

For a (probably) very small set of users, the `keep_file_open` parameter and `nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` will now raise warnings if set to 'auto'. This was scheduled to happen at 2.4.0, but we missed it. Apologies.

Thanks very much to new contributors Egor Pafilov and Jath Palasubramaniam, as well as Richard Nemec and Dave Allured who helped diagnose and provide fixes to some deeply non-obvious bugs.

Full changelog follows.

----

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
(CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC), Paul
McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.

References like "pr/298" refer to github pull request numbers.

2.4.1 (Monday 27 May 2019)
============================

Contributions from Egor Pafilov, Jath Palasubramaniam, Richard Nemec, and
Dave Allured.

Enhancements
------------
* Enable ``mmap``, ``keep_file_open`` options when loading any
  ``DataobjImage`` (pr/759) (CM, reviewed by PM)

Bug fixes
---------
* Ensure loaded GIFTI files expose writable data arrays (pr/750) (CM,
  reviewed by PM)
* Safer warning registry manipulation when checking for overflows (pr/753)
  (CM, reviewed by MB)
* Correctly write .annot files with duplicate lables (pr/763) (Richard Nemec
  with CM)

Maintenance
-----------
* Fix typo in coordinate systems doc (pr/751) (Egor Panfilov, reviewed by
  CM)
* Replace invalid MINC1 test file with fixed file (pr/754) (Dave Allured
  with CM)
* Update Sphinx config to support recent Sphinx/numpydoc (pr/749) (CM,
  reviewed by PM)
* Pacify ``FutureWarning`` and ``DeprecationWarning`` from h5py, numpy
  (pr/760) (CM)
* Accommodate Python 3.8 deprecation of collections.MutableMapping
  (pr/762) (Jath Palasubramaniam, reviewed by CM)

API changes and deprecations
----------------------------
* Deprecate ``keep_file_open == 'auto'`` (pr/761) (CM, reviewed by PM)

--?
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University

From bertrand.thirion at inria.fr  Tue May 28 13:33:19 2019
From: bertrand.thirion at inria.fr (Bertrand Thirion)
Date: Tue, 28 May 2019 19:33:19 +0200 (CEST)
Subject: [Neuroimaging] ANN: nibabel 2.4.1
In-Reply-To: <BN6PR02MB26751349B6E2B528FD6388ADA91E0@BN6PR02MB2675.namprd02.prod.outlook.com>
References: <BN6PR02MB26751349B6E2B528FD6388ADA91E0@BN6PR02MB2675.namprd02.prod.outlook.com>
Message-ID: <944363028.12678906.1559064799826.JavaMail.zimbra@inria.fr>

Thx to all contributors ! 
Best,
Bertrand

----- Mail original -----
> De: "Christopher Markiewicz" <markiewicz at stanford.edu>
> ?: "Neuroimaging analysis in Python" <neuroimaging at python.org>
> Envoy?: Mardi 28 Mai 2019 16:09:57
> Objet: [Neuroimaging] ANN: nibabel 2.4.1

> Hi all,
> 
> Just a quick announcement that nibabel has a new bug-fix release, version 2.4.1.
> The next anticipated release will be 2.5.0, targeted for July, and 2.5.x will
> be the last of the Python 2-compatible series, with bug-fix-only support
> through the *end* of 2020.
> 
> Probably the highest-impact change in 2.4.1 is that all DataobjImages accept the
> `mmap` keyword argument on a best-effort basis, so `nibabel.load(fname,
> mmap=False)` will now succeed for all but GIFTI images. Additionally, GIFTI
> data arrays are editable again with recent numpy, and FreeSurfer annotation
> files can be written more reliably.
> 
> For a (probably) very small set of users, the `keep_file_open` parameter and
> `nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` will now raise warnings if set to
> 'auto'. This was scheduled to happen at 2.4.0, but we missed it. Apologies.
> 
> Thanks very much to new contributors Egor Pafilov and Jath Palasubramaniam, as
> well as Richard Nemec and Dave Allured who helped diagnose and provide fixes to
> some deeply non-obvious bugs.
> 
> Full changelog follows.
> 
> ----
> 
> Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
> (CM), Michael Hanke (MH), Marc-Alexandre C?t? (MC), Ben Cipollini (BC), Paul
> McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
> Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
> 
> References like "pr/298" refer to github pull request numbers.
> 
> 2.4.1 (Monday 27 May 2019)
> ============================
> 
> Contributions from Egor Pafilov, Jath Palasubramaniam, Richard Nemec, and
> Dave Allured.
> 
> Enhancements
> ------------
> * Enable ``mmap``, ``keep_file_open`` options when loading any
>  ``DataobjImage`` (pr/759) (CM, reviewed by PM)
> 
> Bug fixes
> ---------
> * Ensure loaded GIFTI files expose writable data arrays (pr/750) (CM,
>  reviewed by PM)
> * Safer warning registry manipulation when checking for overflows (pr/753)
>  (CM, reviewed by MB)
> * Correctly write .annot files with duplicate lables (pr/763) (Richard Nemec
>  with CM)
> 
> Maintenance
> -----------
> * Fix typo in coordinate systems doc (pr/751) (Egor Panfilov, reviewed by
>  CM)
> * Replace invalid MINC1 test file with fixed file (pr/754) (Dave Allured
>  with CM)
> * Update Sphinx config to support recent Sphinx/numpydoc (pr/749) (CM,
>  reviewed by PM)
> * Pacify ``FutureWarning`` and ``DeprecationWarning`` from h5py, numpy
>  (pr/760) (CM)
> * Accommodate Python 3.8 deprecation of collections.MutableMapping
>  (pr/762) (Jath Palasubramaniam, reviewed by CM)
> 
> API changes and deprecations
> ----------------------------
> * Deprecate ``keep_file_open == 'auto'`` (pr/761) (CM, reviewed by PM)
> 
> --
> Chris Markiewicz
> Center for Reproducible Neuroscience
> Stanford University
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

From matthew.brett at gmail.com  Tue May 28 17:17:29 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Tue, 28 May 2019 22:17:29 +0100
Subject: [Neuroimaging] ANN: nibabel 2.4.1
In-Reply-To: <BN6PR02MB26751349B6E2B528FD6388ADA91E0@BN6PR02MB2675.namprd02.prod.outlook.com>
References: <BN6PR02MB26751349B6E2B528FD6388ADA91E0@BN6PR02MB2675.namprd02.prod.outlook.com>
Message-ID: <CAH6Pt5rdKW3-guuEzzMM-7b+ADjqAS6bG1wT35r2egcw+VVATw@mail.gmail.com>

Hi,

On Tue, May 28, 2019 at 3:10 PM Christopher Markiewicz
<markiewicz at stanford.edu> wrote:
>
> Hi all,
>
> Just a quick announcement that nibabel has a new bug-fix release, version 2.4.1. The next anticipated release will be 2.5.0, targeted for July, and 2.5.x will be the last of the Python 2-compatible series, with bug-fix-only support through the *end* of 2020.
>
> Probably the highest-impact change in 2.4.1 is that all DataobjImages accept the `mmap` keyword argument on a best-effort basis, so `nibabel.load(fname, mmap=False)` will now succeed for all but GIFTI images. Additionally, GIFTI data arrays are editable again with recent numpy, and FreeSurfer annotation files can be written more reliably.
>
> For a (probably) very small set of users, the `keep_file_open` parameter and `nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` will now raise warnings if set to 'auto'. This was scheduled to happen at 2.4.0, but we missed it. Apologies.
>
> Thanks very much to new contributors Egor Pafilov and Jath Palasubramaniam, as well as Richard Nemec and Dave Allured who helped diagnose and provide fixes to some deeply non-obvious bugs.

Great - thanks very much for this.  Thanks too, to Egor, Jath, Richard and Dave,

Cheers,

Matthew

From elef at indiana.edu  Tue May 28 17:32:01 2019
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Tue, 28 May 2019 17:32:01 -0400
Subject: [Neuroimaging] ANN: nibabel 2.4.1
In-Reply-To: <CAH6Pt5rdKW3-guuEzzMM-7b+ADjqAS6bG1wT35r2egcw+VVATw@mail.gmail.com>
References: <BN6PR02MB26751349B6E2B528FD6388ADA91E0@BN6PR02MB2675.namprd02.prod.outlook.com>
 <CAH6Pt5rdKW3-guuEzzMM-7b+ADjqAS6bG1wT35r2egcw+VVATw@mail.gmail.com>
Message-ID: <CAN6JmWNZGX-wxjhCXWLFKGDeE5k4-iMATQuY8WPs=dJ6Q=fDNA@mail.gmail.com>

Super! Thank you all! :)

On Tue, May 28, 2019 at 5:18 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> On Tue, May 28, 2019 at 3:10 PM Christopher Markiewicz
> <markiewicz at stanford.edu> wrote:
> >
> > Hi all,
> >
> > Just a quick announcement that nibabel has a new bug-fix release,
> version 2.4.1. The next anticipated release will be 2.5.0, targeted for
> July, and 2.5.x will be the last of the Python 2-compatible series, with
> bug-fix-only support through the *end* of 2020.
> >
> > Probably the highest-impact change in 2.4.1 is that all DataobjImages
> accept the `mmap` keyword argument on a best-effort basis, so
> `nibabel.load(fname, mmap=False)` will now succeed for all but GIFTI
> images. Additionally, GIFTI data arrays are editable again with recent
> numpy, and FreeSurfer annotation files can be written more reliably.
> >
> > For a (probably) very small set of users, the `keep_file_open` parameter
> and `nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` will now raise warnings if
> set to 'auto'. This was scheduled to happen at 2.4.0, but we missed it.
> Apologies.
> >
> > Thanks very much to new contributors Egor Pafilov and Jath
> Palasubramaniam, as well as Richard Nemec and Dave Allured who helped
> diagnose and provide fixes to some deeply non-obvious bugs.
>
> Great - thanks very much for this.  Thanks too, to Egor, Jath, Richard and
> Dave,
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From Dace.Apsvalka at mrc-cbu.cam.ac.uk  Fri May 31 14:12:54 2019
From: Dace.Apsvalka at mrc-cbu.cam.ac.uk (Dace Apsvalka)
Date: Fri, 31 May 2019 18:12:54 +0000
Subject: [Neuroimaging] PySurfer overlay colour problem
Message-ID: <EE0766F6A04D0D43B7CFE013DB6F508BC0A8FBC8@WSR-EX-01.mrc-cbsu.local>

Hello,

I recently reinstalled PySurfer, and for some reason, the overlay colours are not 'smooth' anymore.

For example, here is how the brain from PySurfer example code looks.
https://photos.app.goo.gl/99eFBUyfXbgRb1Te9

What could be the reason, and what's the solution?

Thanks,
Dace

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