From garyfallidis at gmail.com  Fri May  7 13:14:30 2021
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Fri, 7 May 2021 13:14:30 -0400
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
Message-ID: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>

Hello all,

We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1 are
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 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)


   -

   Release 1.4.1 received contributions from 11 developers (the full
   release notes are at:
   https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).
   -

   Release 1.4.0 received contributions from 8 developers (the full release
   notes are at:
   https://dipy.org/documentation/1.4.0./release_notes/release1.4/).


Thank you all for your contributions and feedback!

Please click here <https://dipy.org/documentation/1.4.1./api_changes/> to
check 1.4.1 API changes.

Please click here <https://dipy.org/documentation/1.4.0./api_changes/> to
check 1.4.0 API changes.

Highlights of 1.4.1 release include:

   -

   New surface seeding module for tractography named mesh.
   -

   Patch2Self and its documentation updated.
   -

   BUAN and RecoBundles documentation updated.
   -

   Standardization and improvement of the multiprocessing / multithreading
   rules.
   -

   Community and governance information added.
   -

   Large update of Cython code in compliance with the last standard.
   -

   Large documentation update.
   -

   Closed 61 issues and merged 28 pull requests.

Highlights of 1.4.0 release include:


   -

   New self-supervised denoising algorithm Patch2Self added.
   -

   Response function refactored and clarified.
   -

   B-tensor allowed with response functions.
   -

   Large Command Line Interface (CLI) documentation updated.
   -

   Public API for Registration added.
   -

   Large documentation update.
   -

   Closed 47 issues and merged 19 pull requests.


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 (0.7.0+).

Questions or suggestions?



For any questions go to https://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

Finally, a new forum is available at
https://github.com/dipy/dipy/discussions

Have a wonderful time using the latest release.


On behalf of the DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

https://dipy.org/contributors
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From satra at mit.edu  Fri May  7 15:01:20 2021
From: satra at mit.edu (Satrajit Ghosh)
Date: Fri, 7 May 2021 15:01:20 -0400
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
In-Reply-To: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
References: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
Message-ID: <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>

congrats dipy folks.

cheers,

satra

On Fri, May 7, 2021 at 1:15 PM Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> Hello all,
>
> We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1
> are 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 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)
>
>
>    -
>
>    Release 1.4.1 received contributions from 11 developers (the full
>    release notes are at:
>    https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).
>    -
>
>    Release 1.4.0 received contributions from 8 developers (the full
>    release notes are at:
>    https://dipy.org/documentation/1.4.0./release_notes/release1.4/).
>
>
> Thank you all for your contributions and feedback!
>
> Please click here <https://dipy.org/documentation/1.4.1./api_changes/> to
> check 1.4.1 API changes.
>
> Please click here <https://dipy.org/documentation/1.4.0./api_changes/> to
> check 1.4.0 API changes.
>
> Highlights of 1.4.1 release include:
>
>    -
>
>    New surface seeding module for tractography named mesh.
>    -
>
>    Patch2Self and its documentation updated.
>    -
>
>    BUAN and RecoBundles documentation updated.
>    -
>
>    Standardization and improvement of the multiprocessing /
>    multithreading rules.
>    -
>
>    Community and governance information added.
>    -
>
>    Large update of Cython code in compliance with the last standard.
>    -
>
>    Large documentation update.
>    -
>
>    Closed 61 issues and merged 28 pull requests.
>
> Highlights of 1.4.0 release include:
>
>
>    -
>
>    New self-supervised denoising algorithm Patch2Self added.
>    -
>
>    Response function refactored and clarified.
>    -
>
>    B-tensor allowed with response functions.
>    -
>
>    Large Command Line Interface (CLI) documentation updated.
>    -
>
>    Public API for Registration added.
>    -
>
>    Large documentation update.
>    -
>
>    Closed 47 issues and merged 19 pull requests.
>
>
> 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 (0.7.0+).
>
> Questions or suggestions?
>
>
>
> For any questions go to https://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
>
> Finally, a new forum is available at
> https://github.com/dipy/dipy/discussions
>
> Have a wonderful time using the latest release.
>
>
> On behalf of the 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 bertrand.thirion at inria.fr  Fri May  7 15:21:24 2021
From: bertrand.thirion at inria.fr (bthirion)
Date: Fri, 7 May 2021 21:21:24 +0200
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
In-Reply-To: <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>
References: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
 <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>
Message-ID: <08986870-877b-0a35-5725-ae67438bbe7b@inria.fr>

Congrats !
Bertrand

On 07/05/2021 21:01, Satrajit Ghosh wrote:
> congrats dipy folks.
>
> cheers,
>
> satra
>
> On Fri, May 7, 2021 at 1:15 PM Eleftherios Garyfallidis 
> <garyfallidis at gmail.com <mailto:garyfallidis at gmail.com>> wrote:
>
>     Hello all,
>
>
>     We are happy to announce two new releases of DIPY: DIPY 1.4.0 and
>     1.4.1 are out!
>
>
>     Please support us by citingDIPY in your papers using the following
>     DOI: 10.3389/fninf.2014.00008
>     <https://www.ncbi.nlm.nih.gov/pubmed/24600385>
>
>
>     DIPY 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)
>
>      *
>
>         Release 1.4.1 received contributions from 11 developers (the
>         full release notes are at:
>         https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).
>
>      *
>
>         Release 1.4.0 received contributions from 8 developers (the
>         full release notes are at:
>         https://dipy.org/documentation/1.4.0./release_notes/release1.4/).
>
>
>     Thank you all for your contributions and feedback!
>
>
>     Please click here
>     <https://dipy.org/documentation/1.4.1./api_changes/>to check 1.4.1
>     API changes.
>
>     Please click here
>     <https://dipy.org/documentation/1.4.0./api_changes/>to check 1.4.0
>     API changes.
>
>
>     Highlights of 1.4.1 release include:
>
>      *
>
>         New surface seeding module for tractography named mesh.
>
>      *
>
>         Patch2Self and its documentation updated.
>
>      *
>
>         BUAN and RecoBundles documentation updated.
>
>      *
>
>         Standardization and improvement of the multiprocessing /
>         multithreading rules.
>
>      *
>
>         Community and governance information added.
>
>      *
>
>         Large update of Cython code in compliance with the last standard.
>
>      *
>
>         Large documentation update.
>
>      *
>
>         Closed 61 issues and merged 28 pull requests.
>
>     Highlights of 1.4.0 release include:
>
>
>      *
>
>         New self-supervised denoising algorithm Patch2Self added.
>
>      *
>
>         Response function refactored and clarified.
>
>      *
>
>         B-tensor allowed with response functions.
>
>      *
>
>         Large Command Line Interface (CLI) documentation updated.
>
>      *
>
>         Public API for Registration added.
>
>      *
>
>         Large documentation update.
>
>      *
>
>         Closed 47 issues and merged 19 pull requests.
>
>
>     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 (0.7.0+).
>
>
>     Questions or suggestions?
>
>     For any questions go to https://dipy.org <https://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/dipy/dipy
>
>     Finally, a new forum is available at
>     https://github.com/dipy/dipy/discussions
>
>
>     Have a wonderful time using the latest release.
>
>
>     On behalf of the DIPY developers,
>
>     Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>
>     https://dipy.org/contributors <https://dipy.org/contributors/>
>
>
>
>
>     _______________________________________________
>     Neuroimaging mailing list
>     Neuroimaging at python.org <mailto: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 markiewicz at stanford.edu  Fri May  7 16:31:16 2021
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Fri, 7 May 2021 20:31:16 +0000
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
In-Reply-To: <08986870-877b-0a35-5725-ae67438bbe7b@inria.fr>
References: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
 <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>,
 <08986870-877b-0a35-5725-ae67438bbe7b@inria.fr>
Message-ID: <MN2PR02MB6752FAE7F6FFBCD92670508FA9579@MN2PR02MB6752.namprd02.prod.outlook.com>

Nice work, dipy team!

Chris

________________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of bthirion <bertrand.thirion at inria.fr>
Sent: Friday, May 7, 2021 3:21 PM
To: neuroimaging at python.org
Subject: Re: [Neuroimaging] ANN: DIPY 1.4.1 Released!

Congrats !
Bertrand

On 07/05/2021 21:01, Satrajit Ghosh wrote:
congrats dipy folks.

cheers,

satra

On Fri, May 7, 2021 at 1:15 PM Eleftherios Garyfallidis <garyfallidis at gmail.com<mailto:garyfallidis at gmail.com>> wrote:

Hello all,


We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1 are 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 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)

  *   Release 1.4.1 received contributions from 11 developers (the full release notes are at: https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).

  *   Release 1.4.0 received contributions from 8 developers (the full release notes are at: https://dipy.org/documentation/1.4.0./release_notes/release1.4/).


Thank you all for your contributions and feedback!


Please click here<https://dipy.org/documentation/1.4.1./api_changes/> to check 1.4.1 API changes.

Please click here<https://dipy.org/documentation/1.4.0./api_changes/> to check 1.4.0 API changes.


Highlights of 1.4.1 release include:

  *   New surface seeding module for tractography named mesh.

  *   Patch2Self and its documentation updated.

  *   BUAN and RecoBundles documentation updated.

  *   Standardization and improvement of the multiprocessing / multithreading rules.

  *   Community and governance information added.

  *   Large update of Cython code in compliance with the last standard.

  *   Large documentation update.

  *   Closed 61 issues and merged 28 pull requests.

Highlights of 1.4.0 release include:


  *   New self-supervised denoising algorithm Patch2Self added.

  *   Response function refactored and clarified.

  *   B-tensor allowed with response functions.

  *   Large Command Line Interface (CLI) documentation updated.

  *   Public API for Registration added.

  *   Large documentation update.

  *   Closed 47 issues and merged 19 pull requests.


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 (0.7.0+).


Questions or suggestions?



For any questions go to https://dipy.org<https://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/dipy/dipy

Finally, a new forum is available at https://github.com/dipy/dipy/discussions


Have a wonderful time using the latest release.


On behalf of the DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

https://dipy.org/contributors<https://dipy.org/contributors/>



_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging



_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging



From alexandre.gramfort at inria.fr  Sat May  8 05:52:26 2021
From: alexandre.gramfort at inria.fr (Alexandre Gramfort)
Date: Sat, 8 May 2021 11:52:26 +0200
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
In-Reply-To: <MN2PR02MB6752FAE7F6FFBCD92670508FA9579@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
 <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>
 <08986870-877b-0a35-5725-ae67438bbe7b@inria.fr>
 <MN2PR02MB6752FAE7F6FFBCD92670508FA9579@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <CADeotZqHgt0thEg7V9Rt=bV0gT=8oaL6vGX1tXkA_YO1mkkyFA@mail.gmail.com>

excellent ! congrats Dipy team !

Alex

PS : mne-python uses dipy internally for its 3D registration. Its robust
packaging and its pythonic API
makes it a pleasure!



On Fri, May 7, 2021 at 11:04 PM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Nice work, dipy team!
>
> Chris
>
> ________________________________________
> From: Neuroimaging <neuroimaging-bounces+markiewicz=
> stanford.edu at python.org> on behalf of bthirion <bertrand.thirion at inria.fr>
> Sent: Friday, May 7, 2021 3:21 PM
> To: neuroimaging at python.org
> Subject: Re: [Neuroimaging] ANN: DIPY 1.4.1 Released!
>
> Congrats !
> Bertrand
>
> On 07/05/2021 21:01, Satrajit Ghosh wrote:
> congrats dipy folks.
>
> cheers,
>
> satra
>
> On Fri, May 7, 2021 at 1:15 PM Eleftherios Garyfallidis <
> garyfallidis at gmail.com<mailto:garyfallidis at gmail.com>> wrote:
>
> Hello all,
>
>
> We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1
> are 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 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)
>
>   *   Release 1.4.1 received contributions from 11 developers (the full
> release notes are at:
> https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).
>
>   *   Release 1.4.0 received contributions from 8 developers (the full
> release notes are at:
> https://dipy.org/documentation/1.4.0./release_notes/release1.4/).
>
>
> Thank you all for your contributions and feedback!
>
>
> Please click here<https://dipy.org/documentation/1.4.1./api_changes/> to
> check 1.4.1 API changes.
>
> Please click here<https://dipy.org/documentation/1.4.0./api_changes/> to
> check 1.4.0 API changes.
>
>
> Highlights of 1.4.1 release include:
>
>   *   New surface seeding module for tractography named mesh.
>
>   *   Patch2Self and its documentation updated.
>
>   *   BUAN and RecoBundles documentation updated.
>
>   *   Standardization and improvement of the multiprocessing /
> multithreading rules.
>
>   *   Community and governance information added.
>
>   *   Large update of Cython code in compliance with the last standard.
>
>   *   Large documentation update.
>
>   *   Closed 61 issues and merged 28 pull requests.
>
> Highlights of 1.4.0 release include:
>
>
>   *   New self-supervised denoising algorithm Patch2Self added.
>
>   *   Response function refactored and clarified.
>
>   *   B-tensor allowed with response functions.
>
>   *   Large Command Line Interface (CLI) documentation updated.
>
>   *   Public API for Registration added.
>
>   *   Large documentation update.
>
>   *   Closed 47 issues and merged 19 pull requests.
>
>
> 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 (0.7.0+).
>
>
> Questions or suggestions?
>
>
>
> For any questions go to https://dipy.org<https://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/dipy/dipy
>
> Finally, a new forum is available at
> https://github.com/dipy/dipy/discussions
>
>
> Have a wonderful time using the latest release.
>
>
> On behalf of the DIPY developers,
>
> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>
> https://dipy.org/contributors<https://dipy.org/contributors/>
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org<mailto:Neuroimaging at python.org>
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org<mailto: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  Sat May  8 15:52:24 2021
From: jbpoline at gmail.com (JB Poline)
Date: Sat, 8 May 2021 15:52:24 -0400
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
In-Reply-To: <CADeotZqHgt0thEg7V9Rt=bV0gT=8oaL6vGX1tXkA_YO1mkkyFA@mail.gmail.com>
References: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
 <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>
 <08986870-877b-0a35-5725-ae67438bbe7b@inria.fr>
 <MN2PR02MB6752FAE7F6FFBCD92670508FA9579@MN2PR02MB6752.namprd02.prod.outlook.com>
 <CADeotZqHgt0thEg7V9Rt=bV0gT=8oaL6vGX1tXkA_YO1mkkyFA@mail.gmail.com>
Message-ID: <CALMaa81PaZKJH=NKJKzycduUXE-eVtTrDRPw+GEPnOrYYk0aKA@mail.gmail.com>

Ditto !!!
JB

On Sat, May 8, 2021 at 5:53 AM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

> excellent ! congrats Dipy team !
>
> Alex
>
> PS : mne-python uses dipy internally for its 3D registration. Its robust
> packaging and its pythonic API
> makes it a pleasure!
>
>
>
> On Fri, May 7, 2021 at 11:04 PM Christopher Markiewicz <
> markiewicz at stanford.edu> wrote:
>
>> Nice work, dipy team!
>>
>> Chris
>>
>> ________________________________________
>> From: Neuroimaging <neuroimaging-bounces+markiewicz=
>> stanford.edu at python.org> on behalf of bthirion <bertrand.thirion at inria.fr
>> >
>> Sent: Friday, May 7, 2021 3:21 PM
>> To: neuroimaging at python.org
>> Subject: Re: [Neuroimaging] ANN: DIPY 1.4.1 Released!
>>
>> Congrats !
>> Bertrand
>>
>> On 07/05/2021 21:01, Satrajit Ghosh wrote:
>> congrats dipy folks.
>>
>> cheers,
>>
>> satra
>>
>> On Fri, May 7, 2021 at 1:15 PM Eleftherios Garyfallidis <
>> garyfallidis at gmail.com<mailto:garyfallidis at gmail.com>> wrote:
>>
>> Hello all,
>>
>>
>> We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1
>> are 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 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)
>>
>>   *   Release 1.4.1 received contributions from 11 developers (the full
>> release notes are at:
>> https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).
>>
>>   *   Release 1.4.0 received contributions from 8 developers (the full
>> release notes are at:
>> https://dipy.org/documentation/1.4.0./release_notes/release1.4/).
>>
>>
>> Thank you all for your contributions and feedback!
>>
>>
>> Please click here<https://dipy.org/documentation/1.4.1./api_changes/> to
>> check 1.4.1 API changes.
>>
>> Please click here<https://dipy.org/documentation/1.4.0./api_changes/> to
>> check 1.4.0 API changes.
>>
>>
>> Highlights of 1.4.1 release include:
>>
>>   *   New surface seeding module for tractography named mesh.
>>
>>   *   Patch2Self and its documentation updated.
>>
>>   *   BUAN and RecoBundles documentation updated.
>>
>>   *   Standardization and improvement of the multiprocessing /
>> multithreading rules.
>>
>>   *   Community and governance information added.
>>
>>   *   Large update of Cython code in compliance with the last standard.
>>
>>   *   Large documentation update.
>>
>>   *   Closed 61 issues and merged 28 pull requests.
>>
>> Highlights of 1.4.0 release include:
>>
>>
>>   *   New self-supervised denoising algorithm Patch2Self added.
>>
>>   *   Response function refactored and clarified.
>>
>>   *   B-tensor allowed with response functions.
>>
>>   *   Large Command Line Interface (CLI) documentation updated.
>>
>>   *   Public API for Registration added.
>>
>>   *   Large documentation update.
>>
>>   *   Closed 47 issues and merged 19 pull requests.
>>
>>
>> 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 (0.7.0+).
>>
>>
>> Questions or suggestions?
>>
>>
>>
>> For any questions go to https://dipy.org<https://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/dipy/dipy
>>
>> Finally, a new forum is available at
>> https://github.com/dipy/dipy/discussions
>>
>>
>> Have a wonderful time using the latest release.
>>
>>
>> On behalf of the DIPY developers,
>>
>> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>>
>> https://dipy.org/contributors<https://dipy.org/contributors/>
>>
>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org<mailto:Neuroimaging at python.org>
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org<mailto: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 garyfallidis at gmail.com  Sat May  8 18:04:39 2021
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Sat, 8 May 2021 18:04:39 -0400
Subject: [Neuroimaging] ANN: DIPY 1.4.1 Released!
In-Reply-To: <775d6436827c41f9993c27d35927c8ef@DM5PR08MB3595.namprd08.prod.outlook.com>
References: <CAN6JmWN7fQwvoATc819j0VgOPegg7cF4DUtUGkguo_SnqLT=qg@mail.gmail.com>
 <CA+A4wOn95_TuuDHvOsfba9XNVOYx=s5mogvN3j3VPU7SWE7J1A@mail.gmail.com>
 <08986870-877b-0a35-5725-ae67438bbe7b@inria.fr>
 <MN2PR02MB6752FAE7F6FFBCD92670508FA9579@MN2PR02MB6752.namprd02.prod.outlook.com>
 <CADeotZqHgt0thEg7V9Rt=bV0gT=8oaL6vGX1tXkA_YO1mkkyFA@mail.gmail.com>
 <775d6436827c41f9993c27d35927c8ef@DM5PR08MB3595.namprd08.prod.outlook.com>
Message-ID: <CAN6JmWNB3pPO5zkj+7WtFu2Fo=St1Mc2yzTLF+-3A8c+a7oSpA@mail.gmail.com>

Thank you all for your encouragement.

DIPY and Neuroimaging in Python overall has gone a long way.

It would be great to have a chat with representative devs from all projects
to summarize new developments across NIPY.org.

Possibly there is plenty of code and APIs to share.

Have a wonderful weekend!
Eleftherios


On Sat, May 8, 2021 at 3:53 PM JB Poline <jbpoline at gmail.com> wrote:

> Ditto !!!
> JB
>
> On Sat, May 8, 2021 at 5:53 AM Alexandre Gramfort <
> alexandre.gramfort at inria.fr> wrote:
>
>> excellent ! congrats Dipy team !
>>
>> Alex
>>
>> PS : mne-python uses dipy internally for its 3D registration. Its robust
>> packaging and its pythonic API
>> makes it a pleasure!
>>
>>
>>
>> On Fri, May 7, 2021 at 11:04 PM Christopher Markiewicz <
>> markiewicz at stanford.edu> wrote:
>>
>>> Nice work, dipy team!
>>>
>>> Chris
>>>
>>> ________________________________________
>>> From: Neuroimaging <neuroimaging-bounces+markiewicz=
>>> stanford.edu at python.org> on behalf of bthirion <
>>> bertrand.thirion at inria.fr>
>>> Sent: Friday, May 7, 2021 3:21 PM
>>> To: neuroimaging at python.org
>>> Subject: Re: [Neuroimaging] ANN: DIPY 1.4.1 Released!
>>>
>>> Congrats !
>>> Bertrand
>>>
>>> On 07/05/2021 21:01, Satrajit Ghosh wrote:
>>> congrats dipy folks.
>>>
>>> cheers,
>>>
>>> satra
>>>
>>> On Fri, May 7, 2021 at 1:15 PM Eleftherios Garyfallidis <
>>> garyfallidis at gmail.com<mailto:garyfallidis at gmail.com>> wrote:
>>>
>>> Hello all,
>>>
>>>
>>> We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1
>>> are 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 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021)
>>>
>>>   *   Release 1.4.1 received contributions from 11 developers (the full
>>> release notes are at:
>>> https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/).
>>>
>>>   *   Release 1.4.0 received contributions from 8 developers (the full
>>> release notes are at:
>>> https://dipy.org/documentation/1.4.0./release_notes/release1.4/).
>>>
>>>
>>> Thank you all for your contributions and feedback!
>>>
>>>
>>> Please click here<https://dipy.org/documentation/1.4.1./api_changes/>
>>> to check 1.4.1 API changes.
>>>
>>> Please click here<https://dipy.org/documentation/1.4.0./api_changes/>
>>> to check 1.4.0 API changes.
>>>
>>>
>>> Highlights of 1.4.1 release include:
>>>
>>>   *   New surface seeding module for tractography named mesh.
>>>
>>>   *   Patch2Self and its documentation updated.
>>>
>>>   *   BUAN and RecoBundles documentation updated.
>>>
>>>   *   Standardization and improvement of the multiprocessing /
>>> multithreading rules.
>>>
>>>   *   Community and governance information added.
>>>
>>>   *   Large update of Cython code in compliance with the last standard.
>>>
>>>   *   Large documentation update.
>>>
>>>   *   Closed 61 issues and merged 28 pull requests.
>>>
>>> Highlights of 1.4.0 release include:
>>>
>>>
>>>   *   New self-supervised denoising algorithm Patch2Self added.
>>>
>>>   *   Response function refactored and clarified.
>>>
>>>   *   B-tensor allowed with response functions.
>>>
>>>   *   Large Command Line Interface (CLI) documentation updated.
>>>
>>>   *   Public API for Registration added.
>>>
>>>   *   Large documentation update.
>>>
>>>   *   Closed 47 issues and merged 19 pull requests.
>>>
>>>
>>> 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 (0.7.0+).
>>>
>>>
>>> Questions or suggestions?
>>>
>>>
>>>
>>> For any questions go to https://dipy.org<https://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/dipy/dipy
>>>
>>> Finally, a new forum is available at
>>> https://github.com/dipy/dipy/discussions
>>>
>>>
>>> Have a wonderful time using the latest release.
>>>
>>>
>>> On behalf of the DIPY developers,
>>>
>>> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>>>
>>> https://dipy.org/contributors<https://dipy.org/contributors/>
>>>
>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org<mailto:Neuroimaging at python.org>
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org<mailto: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 d.soto.b at gmail.com  Thu May 20 05:36:27 2021
From: d.soto.b at gmail.com (David Soto)
Date: Thu, 20 May 2021 11:36:27 +0200
Subject: [Neuroimaging] nipy for doing volume realignment & smoothing in
 real time
Message-ID: <CAPeRSSVAQH9LqeKU2-OSCUETXNhn7xXmwwxo7APh5K=EgEG_RA@mail.gmail.com>

Hi,
we are planning a real time fMRi experiment and would like to use nipy to
do some preprocessing namely volume realignment of each incoming TR + some
smoothing

however by looking at the documentation. E.g:
>>> from nipype.interfaces import fsl>
>> from nipype.testing import example_data
>>> mcflt = fsl.MCFLIRT(in_file=example_data('functional.nii'),
cost='mutualinfo')
>>> res = mcflt.run()

it would seem that it would only work for  a collection of scans (i.e.the
4D file) of a run.

Would there be a way to use nipy tools to have a reference image and then
each scan that is analysed in realtime to be realigned relative to that
reference?

thanks for any feedback/suggestions!

best,
David
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From michiel.cottaar at ndcn.ox.ac.uk  Thu May 20 05:57:46 2021
From: michiel.cottaar at ndcn.ox.ac.uk (Michiel Cottaar)
Date: Thu, 20 May 2021 09:57:46 +0000
Subject: [Neuroimaging] nipy for doing volume realignment & smoothing in
 real time
In-Reply-To: <CAPeRSSVAQH9LqeKU2-OSCUETXNhn7xXmwwxo7APh5K=EgEG_RA@mail.gmail.com>
References: <CAPeRSSVAQH9LqeKU2-OSCUETXNhn7xXmwwxo7APh5K=EgEG_RA@mail.gmail.com>
Message-ID: <C3E870B5-2D3F-4838-B2BD-B17875BD8755@ndcn.ox.ac.uk>

Hi,

There are many registration tools wrapped in nipype you could choose from to register a 3D volume to a reference. Within FSL you could use fsl.FLIRT(in_file='latest_scan.nii', ref='reference.nii) .

Best wishes,

Michiel

On 20 May 2021, at 10:36, David Soto <d.soto.b at gmail.com<mailto:d.soto.b at gmail.com>> wrote:

Hi,
we are planning a real time fMRi experiment and would like to use nipy to do some preprocessing namely volume realignment of each incoming TR + some smoothing

however by looking at the documentation. E.g:
>>> from nipype.interfaces import fsl>
>> from nipype.testing import example_data
>>> mcflt = fsl.MCFLIRT(in_file=example_data('functional.nii'), cost='mutualinfo')
>>> res = mcflt.run()

it would seem that it would only work for  a collection of scans (i.e.the 4D file) of a run.

Would there be a way to use nipy tools to have a reference image and then each scan that is analysed in realtime to be realigned relative to that reference?

thanks for any feedback/suggestions!

best,
David



_______________________________________________
Neuroimaging mailing list
Neuroimaging at python.org<mailto:Neuroimaging at python.org>
https://mail.python.org/mailman/listinfo/neuroimaging

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