From malin.sandstrom at incf.org  Fri Nov  6 14:33:03 2020
From: malin.sandstrom at incf.org (=?UTF-8?Q?Malin_Sandstr=C3=B6m?=)
Date: Fri, 6 Nov 2020 20:33:03 +0100
Subject: [Neuroimaging] Last call for community input on NIDM,
 the neuroimaging data model for task based fMRI
Message-ID: <CAOAt7bbJSt+BKWn7SGnyu9-TK5ybV__t5ExrqsAwb5fM6QhCuQ@mail.gmail.com>

Dear all,

This weekend is the last opportunity to give input and feedback on the
INCF-developed neuroimaging data model, NIDM. This format is accepted into
SPM and FSL, and you can share and visualise your NIDM-Results packs on
DataLad.

If you use any of those tools, your opinion is of interest to us! Don't be
shy to let us know what you think. Community is what makes standards better
for all.

Add your thoughts: NIDMreview <http://bit.ly/NIDMreview>
DOI: 10.7490/f1000research.1117859.1
Find out more about NIDM-Results: NIDM-Rinfo <http://bit.ly/NIDM-Rinfo>
Check out this short video on NIDM-Results: NIDMclip
<http://bit.ly/NIDMclip>
Learn more about why your voice matters: bit.ly/SBPcommunity

Happy weekend!
Malin
-- 
Malin Sandstr?m, PhD
Community Engagement Officer
malin.sandstrom at incf.org

International Neuroinformatics Coordinating Facility
Karolinska Institutet
Nobels v?g 15 A
SE-171 77  Stockholm
Sweden
http://www.incf.org
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From zhengang at sas.upenn.edu  Fri Nov  6 17:26:28 2020
From: zhengang at sas.upenn.edu (Zhengang Lu)
Date: Fri, 6 Nov 2020 17:26:28 -0500
Subject: [Neuroimaging] =?utf-8?q?=5BPySurfer=5D_How_can_I_plot_the_bound?=
	=?utf-8?q?ary_of_a_ROI_defined_by_a_functional_face_localizer?=
	=?utf-8?b?77yf?=
Message-ID: <CAJYL0zvJDboG1siLgVq9mOq2qLZt+Ge4HdivCMi13dWTTRmw4g@mail.gmail.com>

Hi PySurfer gurus,

I just want to show the Fusiform Face Area mask on the surface. But I
didn't find it easy to implement. Did I miss something? Which function
should I use?

Thanks!!

Zhengang
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From larson.eric.d at gmail.com  Mon Nov  9 07:57:17 2020
From: larson.eric.d at gmail.com (Eric Larson)
Date: Mon, 9 Nov 2020 07:57:17 -0500
Subject: [Neuroimaging] 
	=?utf-8?q?=5BPySurfer=5D_How_can_I_plot_the_bound?=
	=?utf-8?q?ary_of_a_ROI_defined_by_a_functional_face_localizer?=
	=?utf-8?b?77yf?=
In-Reply-To: <CAJYL0zvJDboG1siLgVq9mOq2qLZt+Ge4HdivCMi13dWTTRmw4g@mail.gmail.com>
References: <CAJYL0zvJDboG1siLgVq9mOq2qLZt+Ge4HdivCMi13dWTTRmw4g@mail.gmail.com>
Message-ID: <CAGu2niWP3LA5q9JaU_N4s3shc4g2SSX_1k+YnDP7VSTNfcik4w@mail.gmail.com>

Brain.add_label with borders=True should do it:

https://pysurfer.github.io/generated/surfer.Brain.html#surfer.Brain.add_label

Eric


On Sat, Nov 7, 2020 at 4:47 AM Zhengang Lu <zhengang at sas.upenn.edu> wrote:

> Hi PySurfer gurus,
>
> I just want to show the Fusiform Face Area mask on the surface. But I
> didn't find it easy to implement. Did I miss something? Which function
> should I use?
>
> Thanks!!
>
> Zhengang
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From garyfallidis at gmail.com  Tue Nov 10 10:14:21 2020
From: garyfallidis at gmail.com (Eleftherios Garyfallidis)
Date: Tue, 10 Nov 2020 10:14:21 -0500
Subject: [Neuroimaging] ANN: DIPY 1.3.0
Message-ID: <CAN6JmWPepfda=tH5aq5XmVPW+-yeQDwVLSsFsgmt4oFK3dr_WA@mail.gmail.com>

Hello all,

We are excited to announce a new release of DIPY: DIPY 1.3 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 1.3.0 (Wednesday, 3 November 2020)

This release received contributions from 27 developers (the full release
notes are at:
https://dipy.org/documentation/1.3.0./release_notes/release1.3/). Thank you
all for your contributions and feedback!

Please click here <https://dipy.org/documentation/1.3.0./api_changes/> to
check API changes.

Highlights of this release include:

- Gibbs ringing correction 10X faster.

- Spherical harmonics basis definitions updated.

- Added SMT2 metrics from mean signal diffusion kurtosis.

- New interface functions added to the registration module.

- New linear transform added to the registration module.

- New tutorials for DIPY command line interfaces.

- Fixed compatibility issues with different dependencies.

- Tqdm (multiplatform progress bar) dependency added.

- Large documentation update.

- Bundle section highlight from BUAN added in Horizon.

- Closed 134 issues and merged 49 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 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

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  Tue Nov 10 10:59:01 2020
From: satra at mit.edu (Satrajit Ghosh)
Date: Tue, 10 Nov 2020 10:59:01 -0500
Subject: [Neuroimaging] ANN: DIPY 1.3.0
In-Reply-To: <CAN6JmWPepfda=tH5aq5XmVPW+-yeQDwVLSsFsgmt4oFK3dr_WA@mail.gmail.com>
References: <CAN6JmWPepfda=tH5aq5XmVPW+-yeQDwVLSsFsgmt4oFK3dr_WA@mail.gmail.com>
Message-ID: <CA+A4wOk5rsjA8j_vZ0dv6_iFD2WsWKdiU7wwfWjMUbKFJvcRJg@mail.gmail.com>

nice work dipy team!!

cheers,

satra

On Tue, Nov 10, 2020 at 10:15 AM Eleftherios Garyfallidis <
garyfallidis at gmail.com> wrote:

> Hello all,
>
> We are excited to announce a new release of DIPY: DIPY 1.3 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 1.3.0 (Wednesday, 3 November 2020)
>
> This release received contributions from 27 developers (the full release
> notes are at:
> https://dipy.org/documentation/1.3.0./release_notes/release1.3/). Thank
> you all for your contributions and feedback!
>
> Please click here <https://dipy.org/documentation/1.3.0./api_changes/> to
> check API changes.
>
> Highlights of this release include:
>
> - Gibbs ringing correction 10X faster.
>
> - Spherical harmonics basis definitions updated.
>
> - Added SMT2 metrics from mean signal diffusion kurtosis.
>
> - New interface functions added to the registration module.
>
> - New linear transform added to the registration module.
>
> - New tutorials for DIPY command line interfaces.
>
> - Fixed compatibility issues with different dependencies.
>
> - Tqdm (multiplatform progress bar) dependency added.
>
> - Large documentation update.
>
> - Bundle section highlight from BUAN added in Horizon.
>
> - Closed 134 issues and merged 49 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 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
>
> 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 markiewicz at stanford.edu  Tue Nov 10 11:00:47 2020
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Tue, 10 Nov 2020 16:00:47 +0000
Subject: [Neuroimaging] ANN: DIPY 1.3.0
In-Reply-To: <CAN6JmWPepfda=tH5aq5XmVPW+-yeQDwVLSsFsgmt4oFK3dr_WA@mail.gmail.com>
References: <CAN6JmWPepfda=tH5aq5XmVPW+-yeQDwVLSsFsgmt4oFK3dr_WA@mail.gmail.com>
Message-ID: <MN2PR02MB67526FAF422FE89B10063F2FA9E90@MN2PR02MB6752.namprd02.prod.outlook.com>

Congrats, team DIPY!
________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Eleftherios Garyfallidis <garyfallidis at gmail.com>
Sent: Tuesday, November 10, 2020 10:14 AM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: [Neuroimaging] ANN: DIPY 1.3.0


Hello all,


We are excited to announce a new release of DIPY: DIPY 1.3 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 1.3.0 (Wednesday, 3 November 2020)


This release received contributions from 27 developers (the full release notes are at: https://dipy.org/documentation/1.3.0./release_notes/release1.3/). Thank you all for your contributions and feedback!


Please click here<https://dipy.org/documentation/1.3.0./api_changes/> to check API changes.


Highlights of this release include:

- Gibbs ringing correction 10X faster.

- Spherical harmonics basis definitions updated.

- Added SMT2 metrics from mean signal diffusion kurtosis.

- New interface functions added to the registration module.

- New linear transform added to the registration module.

- New tutorials for DIPY command line interfaces.

- Fixed compatibility issues with different dependencies.

- Tqdm (multiplatform progress bar) dependency added.

- Large documentation update.

- Bundle section highlight from BUAN added in Horizon.

- Closed 134 issues and merged 49 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 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


On behalf of the DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

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

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From elef at indiana.edu  Tue Nov 10 11:44:40 2020
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Tue, 10 Nov 2020 11:44:40 -0500
Subject: [Neuroimaging] ANN: DIPY 1.3.0
In-Reply-To: <MN2PR02MB67526FAF422FE89B10063F2FA9E90@MN2PR02MB6752.namprd02.prod.outlook.com>
References: <CAN6JmWPepfda=tH5aq5XmVPW+-yeQDwVLSsFsgmt4oFK3dr_WA@mail.gmail.com>
 <MN2PR02MB67526FAF422FE89B10063F2FA9E90@MN2PR02MB6752.namprd02.prod.outlook.com>
Message-ID: <CAN6JmWODsNgCeRu9DTRUBm6Oa03E1FrRhWAq_KZnrESPXwAiRQ@mail.gmail.com>

Thank you Chris and Satra!

On Tue, Nov 10, 2020 at 11:15 AM Christopher Markiewicz <
markiewicz at stanford.edu> wrote:

> Congrats, team DIPY!
> ------------------------------
> *From:* Neuroimaging <neuroimaging-bounces+markiewicz=
> stanford.edu at python.org> on behalf of Eleftherios Garyfallidis <
> garyfallidis at gmail.com>
> *Sent:* Tuesday, November 10, 2020 10:14 AM
> *To:* Neuroimaging analysis in Python <neuroimaging at python.org>
> *Subject:* [Neuroimaging] ANN: DIPY 1.3.0
>
>
> Hello all,
>
> We are excited to announce a new release of DIPY: DIPY 1.3 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 1.3.0 (Wednesday, 3 November 2020)
>
> This release received contributions from 27 developers (the full release
> notes are at:
> https://dipy.org/documentation/1.3.0./release_notes/release1.3/). Thank
> you all for your contributions and feedback!
>
> Please click here <https://dipy.org/documentation/1.3.0./api_changes/> to
> check API changes.
>
> Highlights of this release include:
>
> - Gibbs ringing correction 10X faster.
>
> - Spherical harmonics basis definitions updated.
>
> - Added SMT2 metrics from mean signal diffusion kurtosis.
>
> - New interface functions added to the registration module.
>
> - New linear transform added to the registration module.
>
> - New tutorials for DIPY command line interfaces.
>
> - Fixed compatibility issues with different dependencies.
>
> - Tqdm (multiplatform progress bar) dependency added.
>
> - Large documentation update.
>
> - Bundle section highlight from BUAN added in Horizon.
>
> - Closed 134 issues and merged 49 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 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
>
> 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 nicolas.pannetier at gmail.com  Tue Nov 10 17:39:42 2020
From: nicolas.pannetier at gmail.com (Nicolas Pannetier)
Date: Tue, 10 Nov 2020 14:39:42 -0800
Subject: [Neuroimaging] Open position(s) at Flywheel - Scientific Solution
 Engineer
Message-ID: <CAFt+-33m0puR7E=i3cqy9UuKo0cVyzsNE=uNUoCE9yWDSTXTRQ@mail.gmail.com>

Dear colleagues,



At Flywheel <https://flywheel.io/>, we are developing a data sharing and
distributed computing platform serving biomedical imaging and life sciences
research. We are hiring
<https://jobs.lever.co/flywheel-2/78bcf30b-504b-4ce4-9162-1cb22bfd28e8> to
grow our Scientific Solutions Engineering team of PhDs and Engineers.



Specifically, we are looking for people with software engineering (e.g.
python, matlab), data analytics (e.g. machine learning, ETL, reproducible
scientific workflows, nipype, BIDS) and a research background in the
medical imaging landscape. Compensation is competitive, company is
inclusive, and we are open to hire remotely (half of us are).



So,

- if you are thinking of transitioning to industry or just looking for a
new endeavor, please have a closer look at our job ad here
<https://jobs.lever.co/flywheel-2/78bcf30b-504b-4ce4-9162-1cb22bfd28e8>.

- If you know someone who is, please forward !

- If you have any questions about the position, or if you?re just curious
about Flywheel, please reach out to careers at flywheel.io.


We really do cool things .



Cheers,

Nicolas

___
Nicolas Pannetier
Senior Scientific Solutions Engineer | Flywheel
m: +1 415 867 6034
www.flywheel.io
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From Jelle.Veraart at nyulangone.org  Mon Nov 23 12:25:02 2020
From: Jelle.Veraart at nyulangone.org (Veraart, Jelle)
Date: Mon, 23 Nov 2020 17:25:02 +0000
Subject: [Neuroimaging] Survey on image preprocessing of Diffusion MRI data
Message-ID: <9da71168360a473b877efec80a50c0a4@nyulangone.org>

Dear Neuroimagers,

Image preprocessing is an essential part of the analysis of diffusion MRI (dMRI) data. In this process, we ultimately aim to improve the visual and statistical interpretation of our dMRI analyses by removing or reducing signal fluctuations that don't have a biophysical origin. Thermal noise, subject motion, and various imaging artifacts have been identified as such sources of unwanted signal fluctuations.

When designing a preprocessing pipeline, hundreds of choices need to be made. It has been demonstrated that various combinations of those choices might impact the outcome of your dMRI analysis significantly. However, few steps to standardization have been taken.

With a survey, we now aim to get some insight in the variability in preprocessing strategies and preferences that have been adopted within our scientific community. The survey is the first part of the "Best practices in dMRI preprocessing" project that has been initiated by the Diffusion Study Group (DSG) of the International Society of Magnetic Resonance in Medicine (ISMRM).

We estimate that completing the survey will take about 7 minutes. We hope that you'll find the time to contribute to this project by following this link https://nyu.qualtrics.com/jfe/form/SV_6m3MpZoTQlEi6kR and answer the questions that we have for you.

For questions about this survey or the "Best Practices in dMRI preprocessing" project, please contact jelle.veraart at nyulangone.org

We'd like to reach as much people as possible, so please share this survey to anyone who might be interested or via social media.


Thanks!

Jelle


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