From elef at indiana.edu  Tue Jun  4 13:52:18 2019
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Tue, 4 Jun 2019 13:52:18 -0400
Subject: [Neuroimaging] [DIPY] DIPY exhibition at OHBM 2019 in Rome
Message-ID: <CAN6JmWPT8dKxHjWpj5rZs+hizNRhmSaS1gPLXTj3B-jdpvfULw@mail.gmail.com>

Hi all,

We are organizing an exhibition at OHBM in Rome this year. If you are
coming to OHBM please make sure to come to our booth and say hi. Our banner
should be clearly visible. We will have more than a few really exciting
demonstrations to show you.

Also if you are a DIPY contributor and attending the event make sure you
sent me an email so I can get you involved with the organization of the
booth. We are also planning for a team party.

So far the booth team includes Rafael, Ariel, Serge, Bramsh and myself. Let
us know if you are coming!

Best,
Eleftherios
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From ntbaovn at gmail.com  Tue Jun  4 14:15:09 2019
From: ntbaovn at gmail.com (Aiden Nguyen)
Date: Wed, 5 Jun 2019 01:15:09 +0700
Subject: [Neuroimaging] [DIPY] DIPY exhibition at OHBM 2019 in Rome
In-Reply-To: <CAN6JmWPT8dKxHjWpj5rZs+hizNRhmSaS1gPLXTj3B-jdpvfULw@mail.gmail.com>
References: <CAN6JmWPT8dKxHjWpj5rZs+hizNRhmSaS1gPLXTj3B-jdpvfULw@mail.gmail.com>
Message-ID: <CAF4C8d+ahxKha9=Se1XnSJXpEAo+ww0tgoeWy=PfqF5X8yDu7Q@mail.gmail.com>

So great Eleftherios,

Hope that I can pass by and see you!


Aiden Nguyen

--
Nguyen Thien Bao, PhD
Director and Founder, HBB Tech, Vietnam
Co-founder, HBB Solutions, Vietnam
Head, R&D Division, Cardano Labo, Vietnam
NeuroInformatics Laboratory (NILab), Fondazione Bruno Kessler (FBK),
Trento, Italy
Centro Interdipartimentale Mente e Cervello (CIMeC), Universita degli Studi
di Trento, Italy
Surgical Planning Laboratory (SPL), Department of Radiology, BWH, Harvard
University, MA, USA
Lecturer, Faculty of Information Technology, University of Technology and
Education, Ho Chi Minh, Vietnam
Email: bao at bwh.harvard.edu or tbnguyen at fbk.eu or baont at
hbbsolution.com or ntbaovn at gmail.com
Fax: +39.0461.283.091
Cellphone:   +1. 857.265.6408 (USA)
                 +39.345.293.1006 (Italy)
                 +84.9.2761.3761 (VietNam)


On Wed, Jun 5, 2019 at 12:53 AM Eleftherios Garyfallidis <elef at indiana.edu>
wrote:

> Hi all,
>
> We are organizing an exhibition at OHBM in Rome this year. If you are
> coming to OHBM please make sure to come to our booth and say hi. Our banner
> should be clearly visible. We will have more than a few really exciting
> demonstrations to show you.
>
> Also if you are a DIPY contributor and attending the event make sure you
> sent me an email so I can get you involved with the organization of the
> booth. We are also planning for a team party.
>
> So far the booth team includes Rafael, Ariel, Serge, Bramsh and myself.
> Let us know if you are coming!
>
> Best,
> Eleftherios
>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From elef at indiana.edu  Wed Jun  5 09:42:46 2019
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Wed, 5 Jun 2019 09:42:46 -0400
Subject: [Neuroimaging] [DIPY] IronTract tractography challenge now open
Message-ID: <CAN6JmWPNtNzwAc0D_H3GEu+=WjP0LCzUEEYV1kh-SuvqD6WOdA@mail.gmail.com>

Hello all,
I am forwarding an email from Anastasia Yendiki on this new tractography
challenge. Looks cool!
Best,
Eleftherios


Dear all - The IronTract tractography challenge is now open. For more
information on challenge tasks, ranking criteria, and how to participate,
please visit: https://irontract.mgh.harvard.edu

There will be 2 winners:

  *   Overall winner: The goal is to find the tractography method that
achieves the highest accuracy possible regardless of diffusion sampling
scheme. You can use the full set of b-values/directions as provided, or
only those that work best for your method of choice.
  *   HCP winner: The goal is to find the tractography method that is best
suited for the 2-shell acquisition scheme that the 6500+ data sets of the
lifespan and disease Human Connectome Project studies are being collected
with.

Are you a developer who wants to showcase the performance of your latest
tractography method? Are you a data analyst who wants to see how the tools
used for your lab's studies compare to other approaches? This is your
chance!

Results will be announced at the IronTract challenge session at MICCAI
2019. Participants will have further opportunities to participate in
publications that will result from the challenge.

The challenge will run on the QMENTA platform. To register and get your
access codes for the platform, please visit:
http://irontract.mgh.harvard.edu/register/

On behalf of the organizers,
Anastasia Yendiki.
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From karla_kort at hotmail.com  Wed Jun  5 09:12:50 2019
From: karla_kort at hotmail.com (Karla Kort)
Date: Wed, 5 Jun 2019 13:12:50 +0000
Subject: [Neuroimaging] first dimension too large
Message-ID: <AM6PR0402MB37331190272A8323A4A30E2FE7160@AM6PR0402MB3733.eurprd04.prod.outlook.com>

Hi,

I am trying to write to a new Nifti file in python, but I get this error when running the script from the commandline: 'UserWarning: Using large vector Freesurfer hack; header will not be compatible with SPM or FSL' And this file does not work. When I run the script in jupyter notebook it doesn't give an error, but the file still still doesn't work and seems empty.  I read online that this is because the first dimension is too large, the dimensions of my data are (498511, 1, 1). So I guess that really is the problem, but I could not find any way to work around this. Is there a way? I do really need the complete file.
Also, is there a way to just replace the data part in a nifti file? I noticed that .set_fdata() is not an existing command.

Kind regards,
Karla
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From matthew.brett at gmail.com  Wed Jun  5 16:05:29 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Wed, 5 Jun 2019 21:05:29 +0100
Subject: [Neuroimaging] first dimension too large
In-Reply-To: <AM6PR0402MB37331190272A8323A4A30E2FE7160@AM6PR0402MB3733.eurprd04.prod.outlook.com>
References: <AM6PR0402MB37331190272A8323A4A30E2FE7160@AM6PR0402MB3733.eurprd04.prod.outlook.com>
Message-ID: <CAH6Pt5qXXsUX_DVkXyJ0=YTDeeX5jjkes0iUvXRc-ozLk6M4Sw@mail.gmail.com>

Hi,

On Wed, Jun 5, 2019 at 8:55 PM Karla Kort <karla_kort at hotmail.com> wrote:
>
> Hi,
>
> I am trying to write to a new Nifti file in python, but I get this error when running the script from the commandline: 'UserWarning: Using large vector Freesurfer hack; header will not be compatible with SPM or FSL' And this file does not work. When I run the script in jupyter notebook it doesn't give an error, but the file still still doesn't work and seems empty.  I read online that this is because the first dimension is too large, the dimensions of my data are (498511, 1, 1). So I guess that really is the problem, but I could not find any way to work around this. Is there a way? I do really need the complete file.

Sorry - the problem lies with the NIfTI format - the data dimensions
are of type "short"

https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h

This is a signed 16-bit integer:

https://en.wikipedia.org/wiki/C_data_types

so the maximum number it can represent is 2^15-1 = 32767, and this is
the largest possible valid size for any dimension.

Can you use NIfTI2 instead?  It's designed to solve this problem.

> Also, is there a way to just replace the data part in a nifti file? I noticed that .set_fdata() is not an existing command.

No - you need to create a new image, as in:

img = nib.load('my_image.nii')
new_img = nib.Nifti1Image(new_data, None, img.header)

Cheers,

Matthew

From ts+ml at rcmd.org  Wed Jun  5 16:40:44 2019
From: ts+ml at rcmd.org (=?UTF-8?Q?Tim_Sch=C3=A4fer?=)
Date: Wed, 5 Jun 2019 22:40:44 +0200 (CEST)
Subject: [Neuroimaging] first dimension too large
In-Reply-To: <AM6PR0402MB37331190272A8323A4A30E2FE7160@AM6PR0402MB3733.eurprd04.prod.outlook.com>
References: <AM6PR0402MB37331190272A8323A4A30E2FE7160@AM6PR0402MB3733.eurprd04.prod.outlook.com>
Message-ID: <380128258.744778.1559767245008@ox.hosteurope.de>

AFAIK this is a limitation of the format, so there is no general way around it. 

However, instead of writing the data into one very long dimension, it can be split over several smaller ones instead (the so-called FreeSurfer hack). But for the resulting file to be of any use, the program reading the file has to be aware of the hack and handle the file accordingly (see, e.g., https://github.com/nipy/nibabel/issues/428).

Can you save in another format, like MGH/MGZ for further analysis? What program has to read the file?

Tim

> On June 5, 2019 at 3:12 PM Karla Kort <karla_kort at hotmail.com> wrote:
> 
> 
> Hi,
> 
> I am trying to write to a new Nifti file in python, but I get this error when running the script from the commandline: 'UserWarning: Using large vector Freesurfer hack; header will not be compatible with SPM or FSL' And this file does not work. When I run the script in jupyter notebook it doesn't give an error, but the file still still doesn't work and seems empty.  I read online that this is because the first dimension is too large, the dimensions of my data are (498511, 1, 1). So I guess that really is the problem, but I could not find any way to work around this. Is there a way? I do really need the complete file.
> Also, is there a way to just replace the data part in a nifti file? I noticed that .set_fdata() is not an existing command.
> 
> Kind regards,
> Karla
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging

--
Dr. Tim Sch?fer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

From arokem at gmail.com  Sat Jun 22 17:58:34 2019
From: arokem at gmail.com (Ariel Rokem)
Date: Sat, 22 Jun 2019 14:58:34 -0700
Subject: [Neuroimaging] Nitime 0.8
Message-ID: <CA+X4w0zm99j6V1-wHdLTPkVedn+rvEaAJAniBUkgyLP4Z80rYQ@mail.gmail.com>

Hi everyone,

You might be interested to know that Nitime 0.8 was just released.

This version fixes several regressions and deprecations that have
accumulated since our last release, and drops Python 2 support along the
way.

Cheers,

Ariel
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From stefanv at berkeley.edu  Sun Jun 23 02:17:28 2019
From: stefanv at berkeley.edu (Stefan van der Walt)
Date: Sat, 22 Jun 2019 23:17:28 -0700
Subject: [Neuroimaging] Nofima/Berkeley/Lund postdoc position: Diffusion MRI
 + DiPy
Message-ID: <20190623061728.3uonmwx6rvzti6ri@carbo>

Nofima, the Norwegian food research institute, is searching for a
candidate for a three-year postdoctoral project from the fall of 2019 at
their Troms? location. The project is in conjunction with UC Berkeley
and Lund University. Start date is negotiable.  The position has an
excellent work-life balance, five-weeks? vacation, and participation in
the state health care system. Troms? draws visitors from around the
globe for the world class hiking, skiing, kayaking and climbing
(https://www.instagram.com/visittromso/?hl=en).

For more information, please contact kate.washburn at nofima.no 

Project Description:

Nearly half of all edible seafood is wasted due to real or perceived
quality problems. Currently, seafood characterization is very
qualitative, which hinders research. The project will use state of the
art MRI methods to develop quantitative descriptors of fish tissue. In
particular, newly developed diffusion tensor imaging methods will be
used to describe tissue structure at multiple length scales.  This
information will be used to improve processing and storage methods to
minimize waste and improve sustainability in the fishing industry. MRI
data will be correlated with hyperspectral imaging data with the aim of
developing high throughput screening techniques.

Responsibilities:

  ? Improving MRI data analysis methods
  ? Use machine learning to relate MRI data to quality attributes
  ? Joint analysis and interpretation of MRI, hyperspectral and wet lab data
  ? Assisting in data acquisition
  ? Incorporating developed methods into the DiPy toolbox for dissemination
  ? Publishing results in relevant academic journals and presenting results at relevant conferences

Qualifications:

  ? Doctoral degree in computer science, machine learning, physics, or other relevant discipline
  ? Experience in programming
  ? Experience in machine learning, image analysis, and neural networks
  ? Experience in magnetic resonance is desirable, but not required
  ? Fluent in both written and spoken English. Knowledge of Norwegian not required
  ? Position will require some travel, and includes an overseas stay at UC Berkeley and at Lund University

From matthew.brett at gmail.com  Sun Jun 23 02:38:04 2019
From: matthew.brett at gmail.com (Matthew Brett)
Date: Sun, 23 Jun 2019 07:38:04 +0100
Subject: [Neuroimaging] Nitime 0.8
In-Reply-To: <CA+X4w0zm99j6V1-wHdLTPkVedn+rvEaAJAniBUkgyLP4Z80rYQ@mail.gmail.com>
References: <CA+X4w0zm99j6V1-wHdLTPkVedn+rvEaAJAniBUkgyLP4Z80rYQ@mail.gmail.com>
Message-ID: <CAH6Pt5pxE-YBJZkkZZDXycOmMOssGAgfbP0ufg1AW8dYSAw6PA@mail.gmail.com>

Many thanks, for the work, and the announcement.

Cheers

Matthew

On Sat, 22 Jun 2019, 22:59 Ariel Rokem, <arokem at gmail.com> wrote:

> Hi everyone,
>
> You might be interested to know that Nitime 0.8 was just released.
>
> This version fixes several regressions and deprecations that have
> accumulated since our last release, and drops Python 2 support along the
> way.
>
> Cheers,
>
> Ariel
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From jbpoline at gmail.com  Sun Jun 23 15:36:53 2019
From: jbpoline at gmail.com (JB Poline)
Date: Sun, 23 Jun 2019 15:36:53 -0400
Subject: [Neuroimaging] Nitime 0.8
In-Reply-To: <CAH6Pt5pxE-YBJZkkZZDXycOmMOssGAgfbP0ufg1AW8dYSAw6PA@mail.gmail.com>
References: <CA+X4w0zm99j6V1-wHdLTPkVedn+rvEaAJAniBUkgyLP4Z80rYQ@mail.gmail.com>
 <CAH6Pt5pxE-YBJZkkZZDXycOmMOssGAgfbP0ufg1AW8dYSAw6PA@mail.gmail.com>
Message-ID: <CALMaa83j4bc7f7-k9ms_Wk211FRY6MsKT_3T7TGpjE3=uQV5ew@mail.gmail.com>

thanks  a lot - this will be useful !

On Sun, Jun 23, 2019 at 2:38 AM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Many thanks, for the work, and the announcement.
>
> Cheers
>
> Matthew
>
> On Sat, 22 Jun 2019, 22:59 Ariel Rokem, <arokem at gmail.com> wrote:
>
>> Hi everyone,
>>
>> You might be interested to know that Nitime 0.8 was just released.
>>
>> This version fixes several regressions and deprecations that have
>> accumulated since our last release, and drops Python 2 support along the
>> way.
>>
>> Cheers,
>>
>> Ariel
>> _______________________________________________
>> 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 markiewicz at stanford.edu  Wed Jun 26 11:35:33 2019
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Wed, 26 Jun 2019 15:35:33 +0000
Subject: [Neuroimaging] Nibabel: Merge window for Python 2-compatible
 features
Message-ID: <BN6PR02MB2675C8CE89C688180E976D08A9E20@BN6PR02MB2675.namprd02.prod.outlook.com>

Hi all,

This is just a heads up that I'm planning to release nibabel 2.5.0 at the end of July. nibabel 2.5.x will be the last series to support Python 2, and all further releases in the series will be bug-fix only. Bug-fix support for 2.5.x will extend to the end of 2020, per the discussion in https://github.com/nipy/nibabel/issues/735.

If there are features that you've been meaning to add, and would like to see supported in Python 2, now is the time to propose them.

I anticipate a nibabel 3.0 release candidate in October, with a full release before the new year. Note that nibabel 3.0 will be Python 3.5+, as Python 3.4 has also reached end-of-life.

Thanks,

--

Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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