From mschendel at mrn.org  Thu Sep  3 17:10:06 2020
From: mschendel at mrn.org (Megan Schendel)
Date: Thu, 3 Sep 2020 15:10:06 -0600
Subject: [Neuroimaging] [DIPY] pip question
Message-ID: <CAEJtD-H_4_q031vLN9tGhQWfktcBFnZNa0Q25=d=ZN_vLs=bfQ@mail.gmail.com>

Hi all,
I am following instructions from the mne python conda environment
<https://mne.tools/stable/install/mne_python.html#installing-mne-python-and-its-dependencies>
to update.  It includes...
dependencies:
- pip:
  - dipy --only-binary dipy

Below is the conda update command, and later, the error when it tries to do
the dipy update.
Should I change the line of the environment.yml file?
FYI, I have a previous installation showing dipy... and your instructions
say to remove that before trying to update.

Does the environment.yml line need to be changed?
Thanks for any help/advice.
Megan Schendel

>From terminal:
conda env update --file environment.yml
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata ...........
Solving package specifications: .
...
ERROR: Invalid requirement: 'dipy --only-binary dipy'

>From python:
>>> import dipy
>>> dipy.__file__
'/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/lib/python3.5/site-packages/dipy/__init__.py'


MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106
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From matthew.brett at gmail.com  Fri Sep  4 04:56:48 2020
From: matthew.brett at gmail.com (Matthew Brett)
Date: Fri, 4 Sep 2020 09:56:48 +0100
Subject: [Neuroimaging] [DIPY] pip question
In-Reply-To: <CAEJtD-H_4_q031vLN9tGhQWfktcBFnZNa0Q25=d=ZN_vLs=bfQ@mail.gmail.com>
References: <CAEJtD-H_4_q031vLN9tGhQWfktcBFnZNa0Q25=d=ZN_vLs=bfQ@mail.gmail.com>
Message-ID: <CAH6Pt5qHYT-aLrGcvtENNcz_L0TZAivXNgiCdvU6HTMCzbTjzw@mail.gmail.com>

Hi,

On Thu, Sep 3, 2020 at 10:29 PM Megan Schendel <mschendel at mrn.org> wrote:
>
> Hi all,
> I am following instructions from the mne python conda environment to update.  It includes...
> dependencies:
> - pip:
>   - dipy --only-binary dipy
>
> Below is the conda update command, and later, the error when it tries to do the dipy update.
> Should I change the line of the environment.yml file?
> FYI, I have a previous installation showing dipy... and your instructions say to remove that before trying to update.
>
> Does the environment.yml line need to be changed?
> Thanks for any help/advice.
> Megan Schendel
>
> From terminal:
> conda env update --file environment.yml
> Using Anaconda Cloud api site https://api.anaconda.org
> Fetching package metadata ...........
> Solving package specifications: .
> ...
> ERROR: Invalid requirement: 'dipy --only-binary dipy'

I don't use conda myself - but I guess that line must be wrong, and
you need to drop either the first or the second 'dipy' , as in:

dependencies:
 - pip:
   - --only-binary dipy

or:

dependencies:
 - pip:
   - dipy --only-binary

Cheers,

Matthew

From mschendel at mrn.org  Fri Sep  4 16:37:30 2020
From: mschendel at mrn.org (Megan Schendel)
Date: Fri, 4 Sep 2020 14:37:30 -0600
Subject: [Neuroimaging] [DIPY] pip question
In-Reply-To: <CAH6Pt5qHYT-aLrGcvtENNcz_L0TZAivXNgiCdvU6HTMCzbTjzw@mail.gmail.com>
References: <CAEJtD-H_4_q031vLN9tGhQWfktcBFnZNa0Q25=d=ZN_vLs=bfQ@mail.gmail.com>
 <CAH6Pt5qHYT-aLrGcvtENNcz_L0TZAivXNgiCdvU6HTMCzbTjzw@mail.gmail.com>
Message-ID: <CAEJtD-E-oBY1bNKFFC5sEy+Yk1GeXUyA6_u8cDKOSbQWzOmAfA@mail.gmail.com>

Hi Mathew,
Thank you for the suggestions, I'll give them a try.

Megan
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106



On Fri, Sep 4, 2020 at 2:57 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> On Thu, Sep 3, 2020 at 10:29 PM Megan Schendel <mschendel at mrn.org> wrote:
> >
> > Hi all,
> > I am following instructions from the mne python conda environment to
> update.  It includes...
> > dependencies:
> > - pip:
> >   - dipy --only-binary dipy
> >
> > Below is the conda update command, and later, the error when it tries to
> do the dipy update.
> > Should I change the line of the environment.yml file?
> > FYI, I have a previous installation showing dipy... and your
> instructions say to remove that before trying to update.
> >
> > Does the environment.yml line need to be changed?
> > Thanks for any help/advice.
> > Megan Schendel
> >
> > From terminal:
> > conda env update --file environment.yml
> > Using Anaconda Cloud api site https://api.anaconda.org
> > Fetching package metadata ...........
> > Solving package specifications: .
> > ...
> > ERROR: Invalid requirement: 'dipy --only-binary dipy'
>
> I don't use conda myself - but I guess that line must be wrong, and
> you need to drop either the first or the second 'dipy' , as in:
>
> dependencies:
>  - pip:
>    - --only-binary dipy
>
> or:
>
> dependencies:
>  - pip:
>    - dipy --only-binary
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From larson.eric.d at gmail.com  Sat Sep  5 12:58:50 2020
From: larson.eric.d at gmail.com (Eric Larson)
Date: Sat, 5 Sep 2020 12:58:50 -0400
Subject: [Neuroimaging] [DIPY] pip question
In-Reply-To: <CAEJtD-E-oBY1bNKFFC5sEy+Yk1GeXUyA6_u8cDKOSbQWzOmAfA@mail.gmail.com>
References: <CAEJtD-H_4_q031vLN9tGhQWfktcBFnZNa0Q25=d=ZN_vLs=bfQ@mail.gmail.com>
 <CAH6Pt5qHYT-aLrGcvtENNcz_L0TZAivXNgiCdvU6HTMCzbTjzw@mail.gmail.com>
 <CAEJtD-E-oBY1bNKFFC5sEy+Yk1GeXUyA6_u8cDKOSbQWzOmAfA@mail.gmail.com>
Message-ID: <CAGu2niXs87HDg06kbRxYPb1awyfXdfQBmi=G1cghiGPRptXrxg@mail.gmail.com>

>
> I don't use conda myself - but I guess that line must be wrong, and
>> you need to drop either the first or the second 'dipy' , as in:
>>
>> dependencies:
>>  - pip:
>>    - --only-binary dipy
>>
>
It looks like for pip, --only-binary requires an argument, namely the list
of packages to only consider binary installations for:

$ pip install --only-binary dipy
ERROR: You must give at least one requirement to install (see "pip
help install")
$ pip install dipy --only-binary
...
--only-binary option requires 1 argument
$ pip install dipy --only-binary dipy
Collecting dipy
  Using cached dipy-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl (7.7 MB)
...

So the command in the requirement.txt file is fine, and actually omitting
the `--only-binary` argument leads to an error.

In this particular case, it turns out that the reason that there was a
failure (seen from another thread) is that the system in question runs
CentOS 6.X, which is incompatible with the build platform used to generate
the dipy wheels.

Eric
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From theaxonlab at gmail.com  Sun Sep  6 04:21:24 2020
From: theaxonlab at gmail.com (Axon Lab)
Date: Sun, 6 Sep 2020 10:21:24 +0200
Subject: [Neuroimaging] PhD Offer announcement
Message-ID: <CABL2bMjUfGdh8=PJkZz4=M+TRSfHAD-T2951x77MTfkcQ0Fezg@mail.gmail.com>

Hello,

We would very much appreciate all the help to disseminate the attached
Ph.D. position description at The Axon Lab in Lausanne (Switzerland). We
are searching for Python enthusiasts in a neuroimaging / computational
neuroscience project.

Best,
Oscar Esteban
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From arokem at gmail.com  Tue Sep  8 12:55:23 2020
From: arokem at gmail.com (Ariel Rokem)
Date: Tue, 8 Sep 2020 09:55:23 -0700
Subject: [Neuroimaging] Please help DIPY!
Message-ID: <CA+X4w0z0CSu3EDE-_M9vPhEs46+0a_Fc_gsLgt2tkeJ5TzGFyQ@mail.gmail.com>

Hi everyone,

If you use DIPY, it would be a great help to us if you could fill out this
(brief!) user survey: https://forms.gle/wPubx9TL9zTNEYT48

Thank you!

On behalf of the DIPY team,

Ariel
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From mschendel at mrn.org  Tue Sep  8 17:09:12 2020
From: mschendel at mrn.org (Megan Schendel)
Date: Tue, 8 Sep 2020 15:09:12 -0600
Subject: [Neuroimaging] [DIPY] pip question
In-Reply-To: <CAGu2niXs87HDg06kbRxYPb1awyfXdfQBmi=G1cghiGPRptXrxg@mail.gmail.com>
References: <CAEJtD-H_4_q031vLN9tGhQWfktcBFnZNa0Q25=d=ZN_vLs=bfQ@mail.gmail.com>
 <CAH6Pt5qHYT-aLrGcvtENNcz_L0TZAivXNgiCdvU6HTMCzbTjzw@mail.gmail.com>
 <CAEJtD-E-oBY1bNKFFC5sEy+Yk1GeXUyA6_u8cDKOSbQWzOmAfA@mail.gmail.com>
 <CAGu2niXs87HDg06kbRxYPb1awyfXdfQBmi=G1cghiGPRptXrxg@mail.gmail.com>
Message-ID: <CAEJtD-E2TciePD8ftiNqKysThiaTJ_h49goKjvC87VBFdrvndQ@mail.gmail.com>

Hi Eric,
Ah, I see.  Thanks for catching that info in the other thread and realizing
it's the same issue!!

Megan
MEG Technician
The Mind Research Network
1101 Yale Blvd. NE
Albuquerque, New Mexico 87106



On Sat, Sep 5, 2020 at 11:00 AM Eric Larson <larson.eric.d at gmail.com> wrote:

> I don't use conda myself - but I guess that line must be wrong, and
>>> you need to drop either the first or the second 'dipy' , as in:
>>>
>>> dependencies:
>>>  - pip:
>>>    - --only-binary dipy
>>>
>>
> It looks like for pip, --only-binary requires an argument, namely the list
> of packages to only consider binary installations for:
>
> $ pip install --only-binary dipy
> ERROR: You must give at least one requirement to install (see "pip help install")
> $ pip install dipy --only-binary
> ...
> --only-binary option requires 1 argument
> $ pip install dipy --only-binary dipy
> Collecting dipy
>   Using cached dipy-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl (7.7 MB)
> ...
>
> So the command in the requirement.txt file is fine, and actually omitting
> the `--only-binary` argument leads to an error.
>
> In this particular case, it turns out that the reason that there was a
> failure (seen from another thread) is that the system in question runs
> CentOS 6.X, which is incompatible with the build platform used to generate
> the dipy wheels.
>
> Eric
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From olivier.colliot at sorbonne-universite.fr  Wed Sep  9 06:09:16 2020
From: olivier.colliot at sorbonne-universite.fr (Olivier Colliot)
Date: Wed, 9 Sep 2020 12:09:16 +0200
Subject: [Neuroimaging] Job offer - Lead developer - Brain Image Analysis
 (Paris, France)
Message-ID: <b37f0e90-a83b-fe39-a365-3aff138b2b69@sorbonne-universite.fr>

Hello,

We are recruiting a lead developer for the open source neuroimaging 
software platform Clinica (www.clinica.run).
Could you please help us circulate the job offer?

Thanks in avance
Olivier Colliot
olivier.colliot at sorbonne-universite.fr

*JOB OFFER *

**

*Lead software developer*

*Brain image analysis*

*Keywords:*Python, neuroimaging, image analysis, medical imaging

*The topic: Clinica ? Open Source software for brain image analysis*

The ARAMIS lab develops the Open Source software Clinica 
(www.clinica.run <http://www.clinica.run>), an end-to-end solution for 
brain image analysis. Clinica allows users to easily analyze large-scale 
clinical studies with advanced computational tools. To that purpose, it 
integrates tools for data management, image preprocessing for different 
modalities (anatomical MRI, diffusion MRI, PET), feature extraction, 
machine learning and statistics. Clinica is distributed freely to the 
scientific community and has 400+ users worldwide. It has been used to 
produce high impact medical publications which have advanced the 
understanding of neurodegenerative diseases such as Alzheimer?s disease, 
fronto-temporal dementia and amyotrophic lateral sclerosis. It is also 
widely used by researchers who apply machine learning to the diagnosis 
of brain diseases.

-Samper-Gonz?lez J, Burgos N, Bottani S, ..., Durrleman S, Evgeniou T, 
Colliot O, Reproducible evaluation of classification methods in 
Alzheimer?s disease: Framework and application to MRI and PET data. 
*/NeuroImage/*, 183:504?21,2018.

-Bertrand A, Wen J, Rinaldi D, Houot M, Sayah S, Camuzat A, Fournier C, 
Fontanella S, Routier A, Couratier P, Pasquier F, Habert M-O, Hannequin 
D, Martinaud O, Caroppo P, Levy R, Dubois B, Brice A, Durrleman S, 
Colliot O, and Le Ber I, Early cognitive, structural and microstructural 
changes in c9orf72 presymptomatic carriers before 40 years of age, *JAMA 
Neurology*, 75(2):236-245, 2018

-Wen J, Thibeau-Sutre E, Diaz-Melo M, ?, Durrleman S, Burgos N, Colliot 
O, Convolutional Neural Networks for Classification of Alzheimer?s 
Disease: Overview and Reproducible Evaluation. */Medical Image 
Analysis/*, 63: 101694, 2020

*Your mission*

You will be the lead software developer of Clinica. As such, you will be 
in charge of:

- development of new features (image processing pipelines, traceability, 
visualization),

- validation of new analytic tools,

- project management (task follow-up, issue tracking, meeting organization),

- software maintenance,

- user support and animation of the community

- contribution to training and dissemination organized with the other 
engineers of the Inria center

In addition, you will be presenting the software at international 
scientific conferences and other events (organized for instance by 
Inria, ICM, CNRS?). Finally, you will contribute to ambitious medical 
studies, by deploying Clinica on large databases of patients, 
contributing to the interpretation of results and providing assistance 
to medical users (internal to the lab and external collaborators).

*A vibrant scientific, technological, clinical and ethical environment*

You will work within the ARAMIS lab (www.aramislab.fr 
<http://www.aramislab.fr>) at the Paris Brain Institute 
(http://www.icm-institute.org), one of the world top research institutes 
for neurosciences. The institute is ideally located at the heart of the 
Piti?-Salp?tri?re hospital, downtown Paris.

The ARAMIS lab, which is also part of Inria (the French National 
Institute for Research in Digital Science and Technology), is dedicated 
to the development of new computational approaches for the analysis of 
large neuroimaging and clinical data sets.

You will be strongly involved in scientific aspects of the work, such as 
discussion of methodological issues and interpretation of results. You 
will interact locally with the PhD students, postdoctoral fellows and 
engineers of the ARAMIS lab, as well as our medical collaborators. You 
will take part in the communications and publications resulting from the 
use of the software.

*Your profile*

-PhD degree or Master+experience in the field of medical imaging

-Strong programming skills in Python

-Knowledge of digital image processing and medical imaging is mandatory

-Experience with neuroimaging data (and with neuroimage analysis 
software, e.g. Nipype, SPM, Freesurfer) would be a strong plus

-Good understanding of the software development process and tools (Git, 
continuous integration, tests)

-Excellent planning and organizational skills

-Good writing skills (documentation, website, scientific articles)

-Good relational and communication skills to interact with users and lab 
members

*Salary: *depending on experience

*Type of contract: *fixed-term contract

*Ready to take up the challenge? *

Send your CV to olivier.colliot at sorbonne-universite.fr 
<mailto:olivier.colliot at sorbonne-universite.fr>and to 
ninon.burgos at icm-institute.org <mailto:ninon.burgos at icm-institute.org> .

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From SyedQasim.Abbas at latrobe.edu.au  Wed Sep  9 07:00:22 2020
From: SyedQasim.Abbas at latrobe.edu.au (Syed Qasim Abbas)
Date: Wed, 9 Sep 2020 11:00:22 +0000
Subject: [Neuroimaging] Job offer - Lead developer - Brain Image
 Analysis (Paris, France)
In-Reply-To: <b37f0e90-a83b-fe39-a365-3aff138b2b69@sorbonne-universite.fr>
References: <b37f0e90-a83b-fe39-a365-3aff138b2b69@sorbonne-universite.fr>
Message-ID: <MEAPR01MB24375665116EA369A39A7E73C8260@MEAPR01MB2437.ausprd01.prod.outlook.com>

Respected Professor Olivier,
Hi,
Can you kindly let me whether this job is available for working remotely? I mean, is it necessary for someone to be in Paris to undertake this job? or someone from around the world can avail this job opportunity and work remotely? Thanks for anticipated response.

Regards
Qasim
PhD scholar



From: Neuroimaging <neuroimaging-bounces+syedqasim.abbas=latrobe.edu.au at python.org> On Behalf Of Olivier Colliot
Sent: Wednesday, 9 September 2020 8:09 PM
To: neuroimaging at python.org
Subject: [Neuroimaging] Job offer - Lead developer - Brain Image Analysis (Paris, France)

Hello,

We are recruiting a lead developer for the open source neuroimaging software platform Clinica (www.clinica.run<http://www.clinica.run>).
Could you please help us circulate the job offer?

Thanks in avance
Olivier Colliot
olivier.colliot at sorbonne-universite.fr<mailto:olivier.colliot at sorbonne-universite.fr>
JOB OFFER

Lead software developer
Brain image analysis


Keywords: Python, neuroimaging, image analysis, medical imaging

The topic: Clinica ? Open Source software for brain image analysis
The ARAMIS lab develops the Open Source software Clinica (www.clinica.run<http://www.clinica.run>), an end-to-end solution for brain image analysis. Clinica allows users to easily analyze large-scale clinical studies with advanced computational tools. To that purpose, it integrates tools for data management, image preprocessing for different modalities (anatomical MRI, diffusion MRI, PET), feature extraction, machine learning and statistics. Clinica is distributed freely to the scientific community and has 400+ users worldwide. It has been used to produce high impact medical publications which have advanced the understanding of neurodegenerative diseases such as Alzheimer?s disease, fronto-temporal dementia and amyotrophic lateral sclerosis. It is also widely used by researchers who apply machine learning to the diagnosis of brain diseases.
-       Samper-Gonz?lez J, Burgos N, Bottani S, ..., Durrleman S, Evgeniou T, Colliot O, Reproducible evaluation of classification methods in Alzheimer?s disease: Framework and application to MRI and PET data. NeuroImage, 183:504?21,2018.

-       Bertrand A, Wen J, Rinaldi D, Houot M, Sayah S, Camuzat A, Fournier C, Fontanella S, Routier A, Couratier P, Pasquier F, Habert M-O, Hannequin D, Martinaud O, Caroppo P, Levy R, Dubois B, Brice A, Durrleman S, Colliot O, and Le Ber I, Early cognitive, structural and microstructural changes in c9orf72 presymptomatic carriers before 40 years of age, JAMA Neurology, 75(2):236-245, 2018
-       Wen J, Thibeau-Sutre E, Diaz-Melo M, ?, Durrleman S, Burgos N, Colliot O, Convolutional Neural Networks for Classification of Alzheimer?s Disease: Overview and Reproducible Evaluation. Medical Image Analysis, 63: 101694, 2020

Your mission
You will be the lead software developer of Clinica. As such, you will be in charge of:
- development of new features (image processing pipelines, traceability, visualization),
- validation of new analytic tools,
- project management (task follow-up, issue tracking, meeting organization),
- software maintenance,
- user support and animation of the community
- contribution to training and dissemination organized with the other engineers of the Inria center
In addition, you will be presenting the software at international scientific conferences and other events (organized for instance by Inria, ICM, CNRS?). Finally, you will contribute to ambitious medical studies, by deploying Clinica on large databases of patients, contributing to the interpretation of results and providing assistance to medical users (internal to the lab and external collaborators).

A vibrant scientific, technological, clinical and ethical environment
You will work within the ARAMIS lab (www.aramislab.fr<http://www.aramislab.fr>) at the Paris Brain Institute (http://www.icm-institute.org<http://www.icm-institute.org>), one of the world top research institutes for neurosciences. The institute is ideally located at the heart of the Piti?-Salp?tri?re hospital, downtown Paris.
The ARAMIS lab, which is also part of Inria (the French National Institute for Research in Digital Science and Technology), is dedicated to the development of new computational approaches for the analysis of large neuroimaging and clinical data sets.
You will be strongly involved in scientific aspects of the work, such as discussion of methodological issues and interpretation of results. You will interact locally with the PhD students, postdoctoral fellows and engineers of the ARAMIS lab, as well as our medical collaborators. You will take part in the communications and publications resulting from the use of the software.

Your profile

-       PhD degree or Master+experience in the field of medical imaging

-       Strong programming skills in Python

-       Knowledge of digital image processing and medical imaging is mandatory

-       Experience with neuroimaging data (and with neuroimage analysis software, e.g. Nipype, SPM, Freesurfer) would be a strong plus

-       Good understanding of the software development process and tools (Git, continuous integration, tests)

-       Excellent planning and organizational skills

-       Good writing skills (documentation, website, scientific articles)

-        Good relational and communication skills to interact with users and lab members

Salary: depending on experience
Type of contract: fixed-term contract

Ready to take up the challenge?
Send your CV to olivier.colliot at sorbonne-universite.fr<mailto:olivier.colliot at sorbonne-universite.fr> and to ninon.burgos at icm-institute.org<mailto:ninon.burgos at icm-institute.org> .







-->
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From garyfallidis at gmail.com  Thu Sep 17 17:23:44 2020
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Thu, 17 Sep 2020 17:23:44 -0400
Subject: [Neuroimaging] ANN: DIPY 1.2.0
Message-ID: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>

Hello all,


We are excited to announce a new release of DIPY: DIPY 1.2 is out!

Please support us by citing DIPY in your papers using the following DOI:
10.3389/fninf.2014.00008  <https://www.ncbi.nlm.nih.gov/pubmed/24600385>

DIPY 1.2.0 (Wednesday, 9 September 2020)

This release received contributions from 27 developers (the full release
notes are at:
https://dipy.org/documentation/1.2.0./release_notes/release1.2/). Thank you
all for your contributions and feedback!

Please click here <https://dipy.org/documentation/1.2.0./api_changes/> to
check API changes.

Highlights of this release include:

- New command line interfaces for group analysis: BUAN.
- Added b-tensor encoding for gradient table.
- Better support for single shell or multi-shell response functions.
- Stats module refactored.
- Numpy's minimum version is 1.2.0.
- Fixed compatibilities with FURY 0.6+, VTK9+, CVXPY 1.1+.
- Added multiple tutorials for DIPY command line interfaces.
- Updated SH basis convention.
- Improved performance of tissue classification.
- Fixed a memory overlap bug (multi_median).
- Large documentation update (typography / references).
- Closed 256 issues and merged 94 pull requests.

Note:

   -

   Have in mind that DIPY does not support Python 2 after version 0.16.0.
   All major Python projects have switched to Python 3. It is time that you
   switch too.



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 (3.0.0+).

For visualization you need FURY (0.6.1+).

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/dipy/dipy <https://gitter.im/nipy/dipy>

On behalf of the 110 DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

https://dipy.org/contributors
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From jbpoline at gmail.com  Thu Sep 17 20:33:28 2020
From: jbpoline at gmail.com (JB Poline)
Date: Thu, 17 Sep 2020 20:33:28 -0400
Subject: [Neuroimaging] ANN: DIPY 1.2.0
In-Reply-To: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
References: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
Message-ID: <CALMaa81ue0cNvE1YSPpk-r-F8p6XkFdrY3CPdTCsSG1KmhdvEQ@mail.gmail.com>

Awesome !

On Thu, Sep 17, 2020 at 7:03 PM Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> Hello all,
>
>
> We are excited to announce a new release of DIPY: DIPY 1.2 is out!
>
> Please support us by citing DIPY in your papers using the following DOI:
> 10.3389/fninf.2014.00008  <https://www.ncbi.nlm.nih.gov/pubmed/24600385>
>
> DIPY 1.2.0 (Wednesday, 9 September 2020)
>
> This release received contributions from 27 developers (the full release
> notes are at:
> https://dipy.org/documentation/1.2.0./release_notes/release1.2/). Thank
> you all for your contributions and feedback!
>
> Please click here <https://dipy.org/documentation/1.2.0./api_changes/> to
> check API changes.
>
> Highlights of this release include:
>
> - New command line interfaces for group analysis: BUAN.
> - Added b-tensor encoding for gradient table.
> - Better support for single shell or multi-shell response functions.
> - Stats module refactored.
> - Numpy's minimum version is 1.2.0.
> - Fixed compatibilities with FURY 0.6+, VTK9+, CVXPY 1.1+.
> - Added multiple tutorials for DIPY command line interfaces.
> - Updated SH basis convention.
> - Improved performance of tissue classification.
> - Fixed a memory overlap bug (multi_median).
> - Large documentation update (typography / references).
> - Closed 256 issues and merged 94 pull requests.
>
> Note:
>
>    -
>
>    Have in mind that DIPY does not support Python 2 after version 0.16.0.
>    All major Python projects have switched to Python 3. It is time that you
>    switch too.
>
>
>
> 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 (3.0.0+).
>
> For visualization you need FURY (0.6.1+).
>
> 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/dipy/dipy <https://gitter.im/nipy/dipy>
>
> On behalf of the 110 DIPY developers,
>
> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>
> https://dipy.org/contributors
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From satra at mit.edu  Thu Sep 17 20:56:26 2020
From: satra at mit.edu (Satrajit Ghosh)
Date: Thu, 17 Sep 2020 20:56:26 -0400
Subject: [Neuroimaging] ANN: DIPY 1.2.0
In-Reply-To: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
References: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
Message-ID: <CA+A4wOnhczw=YQvisAFesHUxWPd2_ZR0OksSe_Q_SqmrA3t=sg@mail.gmail.com>

congrats ! nice work !

cheers,

satra


On Thu, Sep 17, 2020 at 7:03 PM Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> Hello all,
>
>
> We are excited to announce a new release of DIPY: DIPY 1.2 is out!
>
> Please support us by citing DIPY in your papers using the following DOI:
> 10.3389/fninf.2014.00008  <https://www.ncbi.nlm.nih.gov/pubmed/24600385>
>
> DIPY 1.2.0 (Wednesday, 9 September 2020)
>
> This release received contributions from 27 developers (the full release
> notes are at:
> https://dipy.org/documentation/1.2.0./release_notes/release1.2/). Thank
> you all for your contributions and feedback!
>
> Please click here <https://dipy.org/documentation/1.2.0./api_changes/> to
> check API changes.
>
> Highlights of this release include:
>
> - New command line interfaces for group analysis: BUAN.
> - Added b-tensor encoding for gradient table.
> - Better support for single shell or multi-shell response functions.
> - Stats module refactored.
> - Numpy's minimum version is 1.2.0.
> - Fixed compatibilities with FURY 0.6+, VTK9+, CVXPY 1.1+.
> - Added multiple tutorials for DIPY command line interfaces.
> - Updated SH basis convention.
> - Improved performance of tissue classification.
> - Fixed a memory overlap bug (multi_median).
> - Large documentation update (typography / references).
> - Closed 256 issues and merged 94 pull requests.
>
> Note:
>
>    -
>
>    Have in mind that DIPY does not support Python 2 after version 0.16.0.
>    All major Python projects have switched to Python 3. It is time that you
>    switch too.
>
>
>
> 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 (3.0.0+).
>
> For visualization you need FURY (0.6.1+).
>
> 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/dipy/dipy <https://gitter.im/nipy/dipy>
>
> On behalf of the 110 DIPY developers,
>
> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>
> https://dipy.org/contributors
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
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From alexandre.gramfort at inria.fr  Mon Sep 21 09:52:37 2020
From: alexandre.gramfort at inria.fr (Alexandre Gramfort)
Date: Mon, 21 Sep 2020 15:52:37 +0200
Subject: [Neuroimaging] [ANN] MNE-Python 0.21
Message-ID: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>

Hello everyone,


We are very pleased to announce the new 0.21 release of MNE-Python!



A few highlights

============


Visualization

   -

   Mixed and volume source estimates can now be visualized in 3D with
   volumetric rendering.
   -

   Added support for plotting cortex ?flat maps?.
   -

   3D rendering in Jupyter notebooks thanks to a new backend.
   -

   PyVista is now the default 3D backend. Mayavi is no longer required
   (except for coregistration).
   -

   Added support for plotting of covariance topomaps.
   -

   Improvements to 3D dipole plotting with MRI overlay.


Preprocessing

   -

   Added support for eSSS.
   -

   Automated muscle artifact detection.
   -

   ICA.find_bads_ecg() can now automatically determine the threshold for
   the CTPS method.


EEG

   -

   Added support for the Reference Electrode Standardization Technique
   (REST) infinity reference.


fNIRS

   -

   Various improvements to visualization and processing of fNIRS data.


Data reading

   -

   The new function mne.io.read_raw() automatically selects to correct
   reader based on the provided filename
   -

   Support reading of Persyst data format
   -

   Support reading of Nihon Kohden data format
   -

   Support reading of SNIRF data format


Notable API changes

================

   -

   The function mne.preprocessing.mark_flat has been deprecated in favor of
   mne.preprocessing.annotate_flat() to increase API consistency: we now have
   annotate_flat(), annotate_movement(), and annotate_muscle_zscore().
   -

   The default argument meg=True in mne.pick_types() will change to
   meg=False in version 0.22. Please be sure to update your code.


Python 3.6+ is now required

=====================

This release drops support for Python versions before 3.6. Python 3.6 was
released almost 4 years ago, and removing support for earlier versions
allows us to take advantage of some new, helpful language features.


Full changelog

===========

For a full list of improvements and API changes, see:

https://mne.tools/stable/whats_new.html#version-0-21


Find the full documentation at https://mne.tools/
<https://mne.tools/stable/index.html>


Installing the new release

===================


Since quite a few things ? including dependencies ? have changed, we
recommend creating a new environment with a ?fresh? installation. Please
follow the installation instructions on our website:

https://mne.tools/stable/install/mne_python.html


Feedback

========


As usual, we welcome your bug reports, feature requests, critiques, and
contributions. Development takes place on GitHub. If you would like to
contribute, star the project, or just take a peek at the code, visit
https://github.com/mne-tools/mne-python.


You may follow us on Twitter: https://twitter.com/mne_news


We hope you will enjoy the new features and many, many small improvements
we have added, and are looking forward to receiving your feedback.


Stay safe and take care!


The MNE-Python developers



Contributors

==========

MNE-Python is a community-driven project. We are always very happy to
welcome new contributors of code and documentation! 41 people contributed
to this release, and 11 of them contributed for the very first time ? thank
you so much for your time and effort, we truly appreciate it!


This is the list of contributors in alphabetical order (first-time
contributors marked with a ?+?):



   -

   Adam Li
   -

   Adonay Nunes
   -

   Alejandro Weinstein
   -

   Alex Rockhill
   -

   Alexandre Gramfort
   -

   Anton Nikolas Waniek
   -

   Britta Westner
   -

   Christian O'Reilly
   -

   Clemens Brunner
   -

   Daniel McCloy
   -

   Eric Larson
   -

   Evgenii Kalenkovich
   -

   Fede Raimondo
   -

   Guillaume Favelier
   -

   Hubert Banville
   -

   Jeroen Van Der Donckt +
   -

   Johann Benerradi +
   -

   Kyle Mathewson +
   -

   Lau M?ller Andersen +
   -

   Liberty Hamilton +
   -

   Luke Bloy
   -

   Lx37 +
   -

   Mainak Jas
   -

   Marijn van Vliet
   -

   Martin Billinger
   -

   Martin Schulz +
   -

   Martin van Harmelen
   -

   Mikolaj Magnuski
   -

   Olaf Hauk
   -

   Rahul Nadkarni +
   -

   Richard H?chenberger
   -

   Robert Luke
   -

   Sara Sommariva
   -

   Simeon Wong +
   -

   Stefan Appelhoff
   -

   Steven Bierer +
   -

   Svea Marie Meyer +
   -

   Teon Brooks
   -

   Thomas Hartmann
   -

   Yu-Han Luo
   -

   chapochn
   -

   mshader
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From bertrand.thirion at inria.fr  Mon Sep 21 10:22:27 2020
From: bertrand.thirion at inria.fr (bthirion)
Date: Mon, 21 Sep 2020 16:22:27 +0200
Subject: [Neuroimaging] [ANN] MNE-Python 0.21
In-Reply-To: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
References: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
Message-ID: <f78d40d6-0ef3-b2d2-3c80-514196f62f4a@inria.fr>

Congratulations !
Bertrand

On 21/09/2020 15:52, Alexandre Gramfort wrote:
>
> Hello everyone,
>
> *
> *
>
> We are very pleased to announce the new 0.21 release of MNE-Python!
>
> *
>
> *
>
> A few highlights
>
> ============
>
> *
> *
>
> Visualization
>
>  *
>
>     Mixed and volume source estimates can now be visualized in 3D with
>     volumetric rendering.
>
>  *
>
>     Added support for plotting cortex ?flat maps?.
>
>  *
>
>     3D rendering in Jupyter notebooks thanks to a new backend.
>
>  *
>
>     PyVista is now the default 3D backend. Mayavi is no longer
>     required (except for coregistration).
>
>  *
>
>     Added support for plotting of covariance topomaps.
>
>  *
>
>     Improvements to 3D dipole plotting with MRI overlay.
>
> *
> *
>
> Preprocessing
>
>  *
>
>     Added support for eSSS.
>
>  *
>
>     Automated muscle artifact detection.
>
>  *
>
>     ICA.find_bads_ecg() can now automatically determine the threshold
>     for the CTPS method.
>
> *
> *
>
> EEG
>
>  *
>
>     Added support for the Reference Electrode Standardization
>     Technique (REST) infinity reference.
>
> *
> *
>
> fNIRS
>
>  *
>
>     Various improvements to visualization and processing of fNIRS data.
>
> *
> *
>
> Data reading
>
>  *
>
>     The new function mne.io.read_raw() automatically selects to
>     correct reader based on the provided filename
>
>  *
>
>     Support reading of Persyst data format
>
>  *
>
>     Support reading of Nihon Kohden data format
>
>  *
>
>     Support reading of SNIRF data format
>
> *
> *
>
> Notable API changes
>
> ================
>
>  *
>
>     The function mne.preprocessing.mark_flat has been deprecated in
>     favor of mne.preprocessing.annotate_flat() to increase API
>     consistency: we now have annotate_flat(), annotate_movement(), and
>     annotate_muscle_zscore().
>
>  *
>
>     The default argument meg=True in mne.pick_types() will change to
>     meg=False in version 0.22. Please be sure to update your code.
>
> *
> *
>
> Python 3.6+ is now required
>
> =====================
>
> This release drops support for Python versions before 3.6. Python 3.6 
> was released almost 4 years ago, and removing support for earlier 
> versions allows us to take advantage of some new, helpful language 
> features.
>
> *
> *
>
> Full changelog
>
> ===========
>
> For a full list of improvements and API changes, see:
>
> https://mne.tools/stable/whats_new.html#version-0-21
>
> *
> *
>
> Find the full documentation at https://mne.tools/ 
> <https://mne.tools/stable/index.html>
>
> *
> *
>
> Installing the new release
>
> ===================
>
> *
> *
>
> Since quite a few things ? including dependencies ? have changed, we 
> recommend creating a new environment with a ?fresh? installation. 
> Please follow the installation instructions on our website:
>
> https://mne.tools/stable/install/mne_python.html
>
> *
> *
>
> Feedback
>
> ========
>
> *
> *
>
> As usual, we welcome your bug reports, feature requests, critiques, 
> and contributions. Development takes place on GitHub. If you would 
> like to contribute, star the project, or just take a peek at the code, 
> visit https://github.com/mne-tools/mne-python.
>
> *
> *
>
> You may follow us on Twitter:https://twitter.com/mne_news 
> <https://twitter.com/mne_news>
>
> *
> *
>
> We hope you will enjoy the new features and many, many small 
> improvements we have added, and are looking forward to receiving your 
> feedback.
>
> *
> *
>
> Stay safe and take care!
>
> *
> *
>
> The MNE-Python developers
>
> *
>
> *
>
> Contributors
>
> ==========
>
> MNE-Python is a community-driven project. We are always very happy to 
> welcome new contributors of code and documentation! 41 people 
> contributed to this release, and 11 of them contributed for the very 
> first time ? thank you so much for your time and effort, we truly 
> appreciate it!
>
> *
> *
>
> This is the list of contributors in alphabetical order (first-time 
> contributors marked with a ?+?):
>
> *
> *
>
>  *
>
>     Adam Li
>
>  *
>
>     Adonay Nunes
>
>  *
>
>     Alejandro Weinstein
>
>  *
>
>     Alex Rockhill
>
>  *
>
>     Alexandre Gramfort
>
>  *
>
>     Anton Nikolas Waniek
>
>  *
>
>     Britta Westner
>
>  *
>
>     Christian O'Reilly
>
>  *
>
>     Clemens Brunner
>
>  *
>
>     Daniel McCloy
>
>  *
>
>     Eric Larson
>
>  *
>
>     Evgenii Kalenkovich
>
>  *
>
>     Fede Raimondo
>
>  *
>
>     Guillaume Favelier
>
>  *
>
>     Hubert Banville
>
>  *
>
>     Jeroen Van Der Donckt +
>
>  *
>
>     Johann Benerradi +
>
>  *
>
>     Kyle Mathewson +
>
>  *
>
>     Lau M?ller Andersen +
>
>  *
>
>     Liberty Hamilton +
>
>  *
>
>     Luke Bloy
>
>  *
>
>     Lx37 +
>
>  *
>
>     Mainak Jas
>
>  *
>
>     Marijn van Vliet
>
>  *
>
>     Martin Billinger
>
>  *
>
>     Martin Schulz +
>
>  *
>
>     Martin van Harmelen
>
>  *
>
>     Mikolaj Magnuski
>
>  *
>
>     Olaf Hauk
>
>  *
>
>     Rahul Nadkarni +
>
>  *
>
>     Richard H?chenberger
>
>  *
>
>     Robert Luke
>
>  *
>
>     Sara Sommariva
>
>  *
>
>     Simeon Wong +
>
>  *
>
>     Stefan Appelhoff
>
>  *
>
>     Steven Bierer +
>
>  *
>
>     Svea Marie Meyer +
>
>  *
>
>     Teon Brooks
>
>  *
>
>     Thomas Hartmann
>
>  *
>
>     Yu-Han Luo
>
>  *
>
>     chapochn
>
>  *
>
>     mshader
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging


-------------- next part --------------
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From jbpoline at gmail.com  Mon Sep 21 10:56:51 2020
From: jbpoline at gmail.com (JB Poline)
Date: Mon, 21 Sep 2020 10:56:51 -0400
Subject: [Neuroimaging] [ANN] MNE-Python 0.21
In-Reply-To: <f78d40d6-0ef3-b2d2-3c80-514196f62f4a@inria.fr>
References: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
 <f78d40d6-0ef3-b2d2-3c80-514196f62f4a@inria.fr>
Message-ID: <CALMaa82etY7k4O4ExW5JP=6azr2LQapWjGJONH9E6LeotTpHQg@mail.gmail.com>

Congrats indeed!
JB

On Mon, Sep 21, 2020 at 10:22 AM bthirion <bertrand.thirion at inria.fr> wrote:

> Congratulations !
> Bertrand
>
> On 21/09/2020 15:52, Alexandre Gramfort wrote:
>
> Hello everyone,
>
>
> We are very pleased to announce the new 0.21 release of MNE-Python!
>
>
>
> A few highlights
>
> ============
>
>
> Visualization
>
>    -
>
>    Mixed and volume source estimates can now be visualized in 3D with
>    volumetric rendering.
>    -
>
>    Added support for plotting cortex ?flat maps?.
>    -
>
>    3D rendering in Jupyter notebooks thanks to a new backend.
>    -
>
>    PyVista is now the default 3D backend. Mayavi is no longer required
>    (except for coregistration).
>    -
>
>    Added support for plotting of covariance topomaps.
>    -
>
>    Improvements to 3D dipole plotting with MRI overlay.
>
>
> Preprocessing
>
>    -
>
>    Added support for eSSS.
>    -
>
>    Automated muscle artifact detection.
>    -
>
>    ICA.find_bads_ecg() can now automatically determine the threshold for
>    the CTPS method.
>
>
> EEG
>
>    -
>
>    Added support for the Reference Electrode Standardization Technique
>    (REST) infinity reference.
>
>
> fNIRS
>
>    -
>
>    Various improvements to visualization and processing of fNIRS data.
>
>
> Data reading
>
>    -
>
>    The new function mne.io.read_raw() automatically selects to correct
>    reader based on the provided filename
>    -
>
>    Support reading of Persyst data format
>    -
>
>    Support reading of Nihon Kohden data format
>    -
>
>    Support reading of SNIRF data format
>
>
> Notable API changes
>
> ================
>
>    -
>
>    The function mne.preprocessing.mark_flat has been deprecated in favor
>    of mne.preprocessing.annotate_flat() to increase API consistency: we now
>    have annotate_flat(), annotate_movement(), and annotate_muscle_zscore().
>    -
>
>    The default argument meg=True in mne.pick_types() will change to
>    meg=False in version 0.22. Please be sure to update your code.
>
>
> Python 3.6+ is now required
>
> =====================
>
> This release drops support for Python versions before 3.6. Python 3.6 was
> released almost 4 years ago, and removing support for earlier versions
> allows us to take advantage of some new, helpful language features.
>
>
> Full changelog
>
> ===========
>
> For a full list of improvements and API changes, see:
>
> https://mne.tools/stable/whats_new.html#version-0-21
>
>
> Find the full documentation at https://mne.tools/
> <https://mne.tools/stable/index.html>
>
>
> Installing the new release
>
> ===================
>
>
> Since quite a few things ? including dependencies ? have changed, we
> recommend creating a new environment with a ?fresh? installation. Please
> follow the installation instructions on our website:
>
> https://mne.tools/stable/install/mne_python.html
>
>
> Feedback
>
> ========
>
>
> As usual, we welcome your bug reports, feature requests, critiques, and
> contributions. Development takes place on GitHub. If you would like to
> contribute, star the project, or just take a peek at the code, visit
> https://github.com/mne-tools/mne-python.
>
>
> You may follow us on Twitter: https://twitter.com/mne_news
>
>
> We hope you will enjoy the new features and many, many small improvements
> we have added, and are looking forward to receiving your feedback.
>
>
> Stay safe and take care!
>
>
> The MNE-Python developers
>
>
>
> Contributors
>
> ==========
>
> MNE-Python is a community-driven project. We are always very happy to
> welcome new contributors of code and documentation! 41 people contributed
> to this release, and 11 of them contributed for the very first time ? thank
> you so much for your time and effort, we truly appreciate it!
>
>
> This is the list of contributors in alphabetical order (first-time
> contributors marked with a ?+?):
>
>
>
>    -
>
>    Adam Li
>    -
>
>    Adonay Nunes
>    -
>
>    Alejandro Weinstein
>    -
>
>    Alex Rockhill
>    -
>
>    Alexandre Gramfort
>    -
>
>    Anton Nikolas Waniek
>    -
>
>    Britta Westner
>    -
>
>    Christian O'Reilly
>    -
>
>    Clemens Brunner
>    -
>
>    Daniel McCloy
>    -
>
>    Eric Larson
>    -
>
>    Evgenii Kalenkovich
>    -
>
>    Fede Raimondo
>    -
>
>    Guillaume Favelier
>    -
>
>    Hubert Banville
>    -
>
>    Jeroen Van Der Donckt +
>    -
>
>    Johann Benerradi +
>    -
>
>    Kyle Mathewson +
>    -
>
>    Lau M?ller Andersen +
>    -
>
>    Liberty Hamilton +
>    -
>
>    Luke Bloy
>    -
>
>    Lx37 +
>    -
>
>    Mainak Jas
>    -
>
>    Marijn van Vliet
>    -
>
>    Martin Billinger
>    -
>
>    Martin Schulz +
>    -
>
>    Martin van Harmelen
>    -
>
>    Mikolaj Magnuski
>    -
>
>    Olaf Hauk
>    -
>
>    Rahul Nadkarni +
>    -
>
>    Richard H?chenberger
>    -
>
>    Robert Luke
>    -
>
>    Sara Sommariva
>    -
>
>    Simeon Wong +
>    -
>
>    Stefan Appelhoff
>    -
>
>    Steven Bierer +
>    -
>
>    Svea Marie Meyer +
>    -
>
>    Teon Brooks
>    -
>
>    Thomas Hartmann
>    -
>
>    Yu-Han Luo
>    -
>
>    chapochn
>    -
>
>    mshader
>
>
>
> _______________________________________________
> Neuroimaging mailing listNeuroimaging at python.orghttps://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 frakkopesto at gmail.com  Mon Sep 21 11:34:04 2020
From: frakkopesto at gmail.com (Franco Pestilli)
Date: Mon, 21 Sep 2020 10:34:04 -0500
Subject: [Neuroimaging] [ANN] MNE-Python 0.21
In-Reply-To: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
References: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
Message-ID: <E4FC0ED6-3B9C-4CEF-A0A3-00609A723C90@gmail.com>

Congrats!
Franco

> On Sep 21, 2020, at 8:52 AM, Alexandre Gramfort <alexandre.gramfort at inria.fr> wrote:
> 
> Hello everyone,
> 
> We are very pleased to announce the new 0.21 release of MNE-Python!
> 
> 
> A few highlights
> ============
> 
> Visualization
> Mixed and volume source estimates can now be visualized in 3D with volumetric rendering.
> Added support for plotting cortex ?flat maps?.
> 3D rendering in Jupyter notebooks thanks to a new backend.
> PyVista is now the default 3D backend. Mayavi is no longer required (except for coregistration).
> Added support for plotting of covariance topomaps.
> Improvements to 3D dipole plotting with MRI overlay.
> 
> Preprocessing
> Added support for eSSS.
> Automated muscle artifact detection.
> ICA.find_bads_ecg() can now automatically determine the threshold for the CTPS method.
> 
> EEG
> Added support for the Reference Electrode Standardization Technique (REST) infinity reference.
> 
> fNIRS
> Various improvements to visualization and processing of fNIRS data.
> 
> Data reading
> The new function mne.io.read_raw() automatically selects to correct reader based on the provided filename
> Support reading of Persyst data format
> Support reading of Nihon Kohden data format
> Support reading of SNIRF data format
> 
> Notable API changes
> ================
> The function mne.preprocessing.mark_flat has been deprecated in favor of mne.preprocessing.annotate_flat() to increase API consistency: we now have annotate_flat(), annotate_movement(), and annotate_muscle_zscore().
> The default argument meg=True in mne.pick_types() will change to meg=False in version 0.22. Please be sure to update your code.
> 
> Python 3.6+ is now required
> =====================
> This release drops support for Python versions before 3.6. Python 3.6 was released almost 4 years ago, and removing support for earlier versions allows us to take advantage of some new, helpful language features.
> 
> Full changelog
> ===========
> For a full list of improvements and API changes, see:
> https://mne.tools/stable/whats_new.html#version-0-21 <https://mne.tools/stable/whats_new.html#version-0-21>
> 
> Find the full documentation at https://mne.tools/ <https://mne.tools/stable/index.html>
> 
> Installing the new release
> ===================
> 
> Since quite a few things ? including dependencies ? have changed, we recommend creating a new environment with a ?fresh? installation. Please follow the installation instructions on our website:
> https://mne.tools/stable/install/mne_python.html <https://mne.tools/stable/install/mne_python.html>
> 
> Feedback
> ========
> 
> As usual, we welcome your bug reports, feature requests, critiques, and contributions. Development takes place on GitHub. If you would like to contribute, star the project, or just take a peek at the code, visit https://github.com/mne-tools/mne-python <https://github.com/mne-tools/mne-python>.
> 
> You may follow us on Twitter: https://twitter.com/mne_news <https://twitter.com/mne_news>
> 
> We hope you will enjoy the new features and many, many small improvements we have added, and are looking forward to receiving your feedback.
> 
> Stay safe and take care!
> 
> The MNE-Python developers
> 
> 
> Contributors
> ==========
> MNE-Python is a community-driven project. We are always very happy to welcome new contributors of code and documentation! 41 people contributed to this release, and 11 of them contributed for the very first time ? thank you so much for your time and effort, we truly appreciate it!
> 
> This is the list of contributors in alphabetical order (first-time contributors marked with a ?+?):
> 
> Adam Li
> Adonay Nunes
> Alejandro Weinstein
> Alex Rockhill
> Alexandre Gramfort
> Anton Nikolas Waniek
> Britta Westner
> Christian O'Reilly
> Clemens Brunner
> Daniel McCloy
> Eric Larson
> Evgenii Kalenkovich
> Fede Raimondo
> Guillaume Favelier
> Hubert Banville
> Jeroen Van Der Donckt +
> Johann Benerradi +
> Kyle Mathewson +
> Lau M?ller Andersen +
> Liberty Hamilton +
> Luke Bloy
> Lx37 +
> Mainak Jas
> Marijn van Vliet
> Martin Billinger
> Martin Schulz +
> Martin van Harmelen
> Mikolaj Magnuski
> Olaf Hauk
> Rahul Nadkarni +
> Richard H?chenberger
> Robert Luke
> Sara Sommariva
> Simeon Wong +
> Stefan Appelhoff
> Steven Bierer +
> Svea Marie Meyer +
> Teon Brooks
> Thomas Hartmann
> Yu-Han Luo
> chapochn
> mshader
> 
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

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From satra at mit.edu  Mon Sep 21 11:54:36 2020
From: satra at mit.edu (Satrajit Ghosh)
Date: Mon, 21 Sep 2020 11:54:36 -0400
Subject: [Neuroimaging] [ANN] MNE-Python 0.21
In-Reply-To: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
References: <CADeotZrxxrjHAdnwZSS06=caCSiAx31YguwAX4w+s8vFLFJKCA@mail.gmail.com>
Message-ID: <CA+A4wOmsVzDVJScorOjZLePsHmH3cr3Y1qtJOOaYb3YpFxfuVg@mail.gmail.com>

nice work folks! glad to continue to see the vibrant nipy ecosystem.

cheers,

satra

On Mon, Sep 21, 2020 at 9:53 AM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

> Hello everyone,
>
>
> We are very pleased to announce the new 0.21 release of MNE-Python!
>
>
>
> A few highlights
>
> ============
>
>
> Visualization
>
>    -
>
>    Mixed and volume source estimates can now be visualized in 3D with
>    volumetric rendering.
>    -
>
>    Added support for plotting cortex ?flat maps?.
>    -
>
>    3D rendering in Jupyter notebooks thanks to a new backend.
>    -
>
>    PyVista is now the default 3D backend. Mayavi is no longer required
>    (except for coregistration).
>    -
>
>    Added support for plotting of covariance topomaps.
>    -
>
>    Improvements to 3D dipole plotting with MRI overlay.
>
>
> Preprocessing
>
>    -
>
>    Added support for eSSS.
>    -
>
>    Automated muscle artifact detection.
>    -
>
>    ICA.find_bads_ecg() can now automatically determine the threshold for
>    the CTPS method.
>
>
> EEG
>
>    -
>
>    Added support for the Reference Electrode Standardization Technique
>    (REST) infinity reference.
>
>
> fNIRS
>
>    -
>
>    Various improvements to visualization and processing of fNIRS data.
>
>
> Data reading
>
>    -
>
>    The new function mne.io.read_raw() automatically selects to correct
>    reader based on the provided filename
>    -
>
>    Support reading of Persyst data format
>    -
>
>    Support reading of Nihon Kohden data format
>    -
>
>    Support reading of SNIRF data format
>
>
> Notable API changes
>
> ================
>
>    -
>
>    The function mne.preprocessing.mark_flat has been deprecated in favor
>    of mne.preprocessing.annotate_flat() to increase API consistency: we now
>    have annotate_flat(), annotate_movement(), and annotate_muscle_zscore().
>    -
>
>    The default argument meg=True in mne.pick_types() will change to
>    meg=False in version 0.22. Please be sure to update your code.
>
>
> Python 3.6+ is now required
>
> =====================
>
> This release drops support for Python versions before 3.6. Python 3.6 was
> released almost 4 years ago, and removing support for earlier versions
> allows us to take advantage of some new, helpful language features.
>
>
> Full changelog
>
> ===========
>
> For a full list of improvements and API changes, see:
>
> https://mne.tools/stable/whats_new.html#version-0-21
>
>
> Find the full documentation at https://mne.tools/
> <https://mne.tools/stable/index.html>
>
>
> Installing the new release
>
> ===================
>
>
> Since quite a few things ? including dependencies ? have changed, we
> recommend creating a new environment with a ?fresh? installation. Please
> follow the installation instructions on our website:
>
> https://mne.tools/stable/install/mne_python.html
>
>
> Feedback
>
> ========
>
>
> As usual, we welcome your bug reports, feature requests, critiques, and
> contributions. Development takes place on GitHub. If you would like to
> contribute, star the project, or just take a peek at the code, visit
> https://github.com/mne-tools/mne-python.
>
>
> You may follow us on Twitter: https://twitter.com/mne_news
>
>
> We hope you will enjoy the new features and many, many small improvements
> we have added, and are looking forward to receiving your feedback.
>
>
> Stay safe and take care!
>
>
> The MNE-Python developers
>
>
>
> Contributors
>
> ==========
>
> MNE-Python is a community-driven project. We are always very happy to
> welcome new contributors of code and documentation! 41 people contributed
> to this release, and 11 of them contributed for the very first time ? thank
> you so much for your time and effort, we truly appreciate it!
>
>
> This is the list of contributors in alphabetical order (first-time
> contributors marked with a ?+?):
>
>
>
>    -
>
>    Adam Li
>    -
>
>    Adonay Nunes
>    -
>
>    Alejandro Weinstein
>    -
>
>    Alex Rockhill
>    -
>
>    Alexandre Gramfort
>    -
>
>    Anton Nikolas Waniek
>    -
>
>    Britta Westner
>    -
>
>    Christian O'Reilly
>    -
>
>    Clemens Brunner
>    -
>
>    Daniel McCloy
>    -
>
>    Eric Larson
>    -
>
>    Evgenii Kalenkovich
>    -
>
>    Fede Raimondo
>    -
>
>    Guillaume Favelier
>    -
>
>    Hubert Banville
>    -
>
>    Jeroen Van Der Donckt +
>    -
>
>    Johann Benerradi +
>    -
>
>    Kyle Mathewson +
>    -
>
>    Lau M?ller Andersen +
>    -
>
>    Liberty Hamilton +
>    -
>
>    Luke Bloy
>    -
>
>    Lx37 +
>    -
>
>    Mainak Jas
>    -
>
>    Marijn van Vliet
>    -
>
>    Martin Billinger
>    -
>
>    Martin Schulz +
>    -
>
>    Martin van Harmelen
>    -
>
>    Mikolaj Magnuski
>    -
>
>    Olaf Hauk
>    -
>
>    Rahul Nadkarni +
>    -
>
>    Richard H?chenberger
>    -
>
>    Robert Luke
>    -
>
>    Sara Sommariva
>    -
>
>    Simeon Wong +
>    -
>
>    Stefan Appelhoff
>    -
>
>    Steven Bierer +
>    -
>
>    Svea Marie Meyer +
>    -
>
>    Teon Brooks
>    -
>
>    Thomas Hartmann
>    -
>
>    Yu-Han Luo
>    -
>
>    chapochn
>    -
>
>    mshader
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From code at oscaresteban.es  Wed Sep 23 05:31:00 2020
From: code at oscaresteban.es (Oscar Esteban)
Date: Wed, 23 Sep 2020 11:31:00 +0200
Subject: [Neuroimaging] ANN: DIPY 1.2.0
In-Reply-To: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
References: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
Message-ID: <CAAsFcgxjDG1Un4sUH2x0R8HuGBJFwAtsFN699_XBRab=Yfh7Gw@mail.gmail.com>

Congratulations!!

Does this release contain Ariel's work on image registration?

Cheers,
Oscar


On Fri, Sep 18, 2020 at 1:03 AM Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> Hello all,
>
>
> We are excited to announce a new release of DIPY: DIPY 1.2 is out!
>
> Please support us by citing DIPY in your papers using the following DOI:
> 10.3389/fninf.2014.00008  <https://www.ncbi.nlm.nih.gov/pubmed/24600385>
>
> DIPY 1.2.0 (Wednesday, 9 September 2020)
>
> This release received contributions from 27 developers (the full release
> notes are at:
> https://dipy.org/documentation/1.2.0./release_notes/release1.2/). Thank
> you all for your contributions and feedback!
>
> Please click here <https://dipy.org/documentation/1.2.0./api_changes/> to
> check API changes.
>
> Highlights of this release include:
>
> - New command line interfaces for group analysis: BUAN.
> - Added b-tensor encoding for gradient table.
> - Better support for single shell or multi-shell response functions.
> - Stats module refactored.
> - Numpy's minimum version is 1.2.0.
> - Fixed compatibilities with FURY 0.6+, VTK9+, CVXPY 1.1+.
> - Added multiple tutorials for DIPY command line interfaces.
> - Updated SH basis convention.
> - Improved performance of tissue classification.
> - Fixed a memory overlap bug (multi_median).
> - Large documentation update (typography / references).
> - Closed 256 issues and merged 94 pull requests.
>
> Note:
>
>    -
>
>    Have in mind that DIPY does not support Python 2 after version 0.16.0.
>    All major Python projects have switched to Python 3. It is time that you
>    switch too.
>
>
>
> 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 (3.0.0+).
>
> For visualization you need FURY (0.6.1+).
>
> 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/dipy/dipy <https://gitter.im/nipy/dipy>
>
> On behalf of the 110 DIPY developers,
>
> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>
> https://dipy.org/contributors
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From arokem at uw.edu  Wed Sep 23 09:34:41 2020
From: arokem at uw.edu (Ariel Rokem)
Date: Wed, 23 Sep 2020 06:34:41 -0700
Subject: [Neuroimaging] ANN: DIPY 1.2.0
In-Reply-To: <CAAsFcgxjDG1Un4sUH2x0R8HuGBJFwAtsFN699_XBRab=Yfh7Gw@mail.gmail.com>
References: <CAN6JmWOT+KKi0wqbMK_Uo4_fV+Hz844f5CKoi+sLV1+uqdAcwA@mail.gmail.com>
 <CAAsFcgxjDG1Un4sUH2x0R8HuGBJFwAtsFN699_XBRab=Yfh7Gw@mail.gmail.com>
Message-ID: <CA+X4w0ycRvEXHgmYupoM4e+1S3LZQxAOFnc0XWAUger=rK-ixA@mail.gmail.com>

On Wed, Sep 23, 2020 at 2:31 AM Oscar Esteban <code at oscaresteban.es> wrote:

> Congratulations!!
>
> Does this release contain Ariel's work on image registration?
>
> Sadly, no. This is still something I have to finish here:
https://github.com/dipy/dipy/pull/2025


> Cheers,
> Oscar
>
>
> On Fri, Sep 18, 2020 at 1:03 AM Eleftherios Garyfallidis <
> garyfallidis at gmail.com> wrote:
>
>> Hello all,
>>
>>
>> We are excited to announce a new release of DIPY: DIPY 1.2 is out!
>>
>> Please support us by citing DIPY in your papers using the following DOI:
>> 10.3389/fninf.2014.00008  <https://www.ncbi.nlm.nih.gov/pubmed/24600385>
>>
>> DIPY 1.2.0 (Wednesday, 9 September 2020)
>>
>> This release received contributions from 27 developers (the full release
>> notes are at:
>> https://dipy.org/documentation/1.2.0./release_notes/release1.2/). Thank
>> you all for your contributions and feedback!
>>
>> Please click here <https://dipy.org/documentation/1.2.0./api_changes/>
>> to check API changes.
>>
>> Highlights of this release include:
>>
>> - New command line interfaces for group analysis: BUAN.
>> - Added b-tensor encoding for gradient table.
>> - Better support for single shell or multi-shell response functions.
>> - Stats module refactored.
>> - Numpy's minimum version is 1.2.0.
>> - Fixed compatibilities with FURY 0.6+, VTK9+, CVXPY 1.1+.
>> - Added multiple tutorials for DIPY command line interfaces.
>> - Updated SH basis convention.
>> - Improved performance of tissue classification.
>> - Fixed a memory overlap bug (multi_median).
>> - Large documentation update (typography / references).
>> - Closed 256 issues and merged 94 pull requests.
>>
>> Note:
>>
>>    -
>>
>>    Have in mind that DIPY does not support Python 2 after version
>>    0.16.0. All major Python projects have switched to Python 3. It is time
>>    that you switch too.
>>
>>
>>
>> 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 (3.0.0+).
>>
>> For visualization you need FURY (0.6.1+).
>>
>> 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/dipy/dipy <https://gitter.im/nipy/dipy>
>>
>> On behalf of the 110 DIPY developers,
>>
>> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>>
>> https://dipy.org/contributors
>>
>> _______________________________________________
>> 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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