From J.Necus2 at newcastle.ac.uk  Fri May 12 12:16:21 2017
From: J.Necus2 at newcastle.ac.uk (Joe Necus (PGR))
Date: Fri, 12 May 2017 16:16:21 +0000
Subject: [Neuroimaging] dipy model fit question
References: <DB4PR07MB0671DCD672486CB90366BB198EE20@DB4PR07MB0671.eurprd07.prod.outlook.com>
Message-ID: <WM!d3a156de0a0418245ccf6c6724b7f3f5faa052d9af20c5ac2b01334c8307634ef75de5227e92e314cc3b9826ef717584!@mailhub-mx2.ncl.ac.uk>

Hello,


I am just starting out with dipy and have a simple question.


After generating my mask and fitting a tensort model, the FA image which I obtain is reduced in size from the original image (as the background is clipped).


I would like to obtain the fa map back in the original data shape, is this possible?


Thanks,

Joe
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From arokem at gmail.com  Sun May 14 20:30:37 2017
From: arokem at gmail.com (Ariel Rokem)
Date: Sun, 14 May 2017 17:30:37 -0700
Subject: [Neuroimaging] dipy model fit question
In-Reply-To: <WM!d3a156de0a0418245ccf6c6724b7f3f5faa052d9af20c5ac2b01334c8307634ef75de5227e92e314cc3b9826ef717584!@mailhub-mx2.ncl.ac.uk>
References: <DB4PR07MB0671DCD672486CB90366BB198EE20@DB4PR07MB0671.eurprd07.prod.outlook.com>
 <WM!d3a156de0a0418245ccf6c6724b7f3f5faa052d9af20c5ac2b01334c8307634ef75de5227e92e314cc3b9826ef717584!@mailhub-mx2.ncl.ac.uk>
Message-ID: <CA+X4w0z8Xcu6Lrw-Q-6XnDBPd_rEOBhVQ6_zkTxxB_sdKCQ=JA@mail.gmail.com>

Hi Joe,

Would you mind posting the code that you ran? I am not sure that I
understand what you mean by "the background is clipped".

Thanks!

Ariel

On Fri, May 12, 2017 at 9:16 AM, Joe Necus (PGR) <J.Necus2 at newcastle.ac.uk>
wrote:

> Hello,
>
>
> I am just starting out with dipy and have a simple question.
>
>
> After generating my mask and fitting a tensort model, the FA image which I
> obtain is reduced in size from the original image (as the background is
> clipped).
>
>
> I would like to obtain the fa map back in the original data shape, is this
> possible?
>
>
> Thanks,
>
> Joe
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
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From elef at indiana.edu  Sun May 14 20:38:00 2017
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Mon, 15 May 2017 00:38:00 +0000
Subject: [Neuroimaging] dipy model fit question
In-Reply-To: <CA+X4w0z8Xcu6Lrw-Q-6XnDBPd_rEOBhVQ6_zkTxxB_sdKCQ=JA@mail.gmail.com>
References: <DB4PR07MB0671DCD672486CB90366BB198EE20@DB4PR07MB0671.eurprd07.prod.outlook.com>
 <WM!d3a156de0a0418245ccf6c6724b7f3f5faa052d9af20c5ac2b01334c8307634ef75de5227e92e314cc3b9826ef717584!@mailhub-mx2.ncl.ac.uk>
 <CA+X4w0z8Xcu6Lrw-Q-6XnDBPd_rEOBhVQ6_zkTxxB_sdKCQ=JA@mail.gmail.com>
Message-ID: <CAN6JmWOQzCN135BeJOnegy7qsKW9mDNTZyU+=m=goY+mxaYVEw@mail.gmail.com>

The fitting cannot reduce the size of the image. Maybe you used median_otsu
with autocrop True.

On Sun, May 14, 2017 at 8:31 PM Ariel Rokem <arokem at gmail.com> wrote:

> Hi Joe,
>
> Would you mind posting the code that you ran? I am not sure that I
> understand what you mean by "the background is clipped".
>
> Thanks!
>
> Ariel
>
> On Fri, May 12, 2017 at 9:16 AM, Joe Necus (PGR) <J.Necus2 at newcastle.ac.uk
> > wrote:
>
>> Hello,
>>
>>
>> I am just starting out with dipy and have a simple question.
>>
>>
>> After generating my mask and fitting a tensort model, the FA image which
>> I obtain is reduced in size from the original image (as the background is
>> clipped).
>>
>>
>> I would like to obtain the fa map back in the original data shape, is
>> this possible?
>>
>>
>> Thanks,
>>
>> Joe
>>
>> _______________________________________________
>> 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 J.Necus2 at newcastle.ac.uk  Mon May 15 03:44:25 2017
From: J.Necus2 at newcastle.ac.uk (Joe Necus (PGR))
Date: Mon, 15 May 2017 07:44:25 +0000
Subject: [Neuroimaging] dipy model fit question
In-Reply-To: <WM!600f3251a0f9ca3acab5b0f54c78b4d4bd1e0cbca233b0863c622ec940925a75b6e431b5d3e8af8c2a0665c0bb21164f!@mailhub-mx4.ncl.ac.uk>
References: <DB4PR07MB0671DCD672486CB90366BB198EE20@DB4PR07MB0671.eurprd07.prod.outlook.com>
 <WM!d3a156de0a0418245ccf6c6724b7f3f5faa052d9af20c5ac2b01334c8307634ef75de5227e92e314cc3b9826ef717584!@mailhub-mx2.ncl.ac.uk>
 <CA+X4w0z8Xcu6Lrw-Q-6XnDBPd_rEOBhVQ6_zkTxxB_sdKCQ=JA@mail.gmail.com>
 <CAN6JmWOQzCN135BeJOnegy7qsKW9mDNTZyU+=m=goY+mxaYVEw@mail.gmail.com>,
 <WM!600f3251a0f9ca3acab5b0f54c78b4d4bd1e0cbca233b0863c622ec940925a75b6e431b5d3e8af8c2a0665c0bb21164f!@mailhub-mx4.ncl.ac.uk>
 <DB4PR07MB067127043697C8ABDCA024A38EE10@DB4PR07MB0671.eurprd07.prod.outlook.com>
Message-ID: <WM!bc85fe6f382146442fd453b5cdd7d093e0109447b3eb567202d477dd77b569ae28f71b041d43bb12d8ce0e39a907a6ca!@mailhub-mx4.ncl.ac.uk>

Hello,


Thank for your reply.


I was indeed using the median_otsu 'autocrop=True' option. By choosing 'False' I can ensure that my output images are maintained at the same dimensions as the original image.


I assume that the advantage of cropping the images is to reduce processing time.


Thanks,

Joe

________________________________
From: Neuroimaging <neuroimaging-bounces+j.necus2=ncl.ac.uk at python.org> on behalf of Eleftherios Garyfallidis <elef at indiana.edu>
Sent: 15 May 2017 01:38:00
To: Neuroimaging analysis in Python
Subject: Re: [Neuroimaging] dipy model fit question

The fitting cannot reduce the size of the image. Maybe you used median_otsu with autocrop True.

On Sun, May 14, 2017 at 8:31 PM Ariel Rokem <arokem at gmail.com<mailto:arokem at gmail.com>> wrote:
Hi Joe,

Would you mind posting the code that you ran? I am not sure that I understand what you mean by "the background is clipped".

Thanks!

Ariel

On Fri, May 12, 2017 at 9:16 AM, Joe Necus (PGR) <J.Necus2 at newcastle.ac.uk<mailto:J.Necus2 at newcastle.ac.uk>> wrote:

Hello,


I am just starting out with dipy and have a simple question.


After generating my mask and fitting a tensort model, the FA image which I obtain is reduced in size from the original image (as the background is clipped).


I would like to obtain the fa map back in the original data shape, is this possible?


Thanks,

Joe

_______________________________________________
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
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From jrudascas at gmail.com  Wed May 17 18:29:42 2017
From: jrudascas at gmail.com (Jorge Rudas)
Date: Wed, 17 May 2017 17:29:42 -0500
Subject: [Neuroimaging] Covert .trk to JSON
Message-ID: <CAOXSzBAE0d7G0Y6e4Yowudq0YCjG4=BmmOMLB05=tzQXe8R_Vw@mail.gmail.com>

Hi dipy experts

There is a direct way to covert a tractography file in .trk format to JSON
format?

Cheers

*Jorge Rudas*
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From elef at indiana.edu  Wed May 17 22:12:49 2017
From: elef at indiana.edu (Eleftherios Garyfallidis)
Date: Thu, 18 May 2017 02:12:49 +0000
Subject: [Neuroimaging] Covert .trk to JSON
In-Reply-To: <CAOXSzBAE0d7G0Y6e4Yowudq0YCjG4=BmmOMLB05=tzQXe8R_Vw@mail.gmail.com>
References: <CAOXSzBAE0d7G0Y6e4Yowudq0YCjG4=BmmOMLB05=tzQXe8R_Vw@mail.gmail.com>
Message-ID: <CAN6JmWOa6ROQchmTi84XgP8+nLNf66rGmWsx9+PP5Z2amox00A@mail.gmail.com>

Hi Jorge,

With the new API for streamlines available in nibabel.streamlines you can
load .trk files and then get all the points of all the streamlines in one
buffer and in another the offsets (starting points) and lenghts of each
streamline.

Here is how
trkfile = nib.streamlines.load('test.trk')
streamlines = trkfile.streamlines
all_points = streamlines.data
offsets = streamlines._offsets
lengths = streamlines._lengths

You can probably save these 3 arrays in a json file with no problem. You
may also want to save the affine. You can get this from trkfile.affine.

I hope this helps.
Best,
Eleftherios

On Wed, May 17, 2017 at 6:30 PM Jorge Rudas <jrudascas at gmail.com> wrote:

> Hi dipy experts
>
> There is a direct way to covert a tractography file in .trk format to JSON
> format?
>
> Cheers
>
> *Jorge Rudas*
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
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From ragini.verma at gmail.com  Wed May 24 17:37:24 2017
From: ragini.verma at gmail.com (Ragini Verma)
Date: Wed, 24 May 2017 17:37:24 -0400
Subject: [Neuroimaging] Postdoc in Connectomics at UPenn
Message-ID: <CALyBJGhX66Gd2fjGrR=Rx5FN7MwYgn07U8HiK1U63wcPj8Oepg@mail.gmail.com>

Postdoctoral positions in diffusion imaging are available immediately at
the Section of Biomedical Image Analysis (SBIA), Department of Radiology,
University of Pennsylvania, Philadelphia, PA, USA. Candidates must have a
background in Electrical or Biomedical Engineering, Computer Science,
Applied Math or MR Physics, with experience in diffusion imaging. Knowledge
of maine learning techniques is a plus. Current projects involve work on
connectomics, multi-compartment models, edema-invariant tractography and
joint structural-functional connectivity analysis and their application
to brain tumors, traumatic brain injury and autism.  Good programming
skills is a must. All projects have a strong emphasis on method development
(for technical publications) but require subsequent clinical application of
the same. The positions call for interaction with clinical collaborators.
Please contact the head of the diffusion group, Ragini Verma (Associate
Professor of Radiology) at Ragini.Verma at gmail.com and
Ragini.Verma at uphs.upenn.edu
<https://mail.uphs.upenn.edu/owa/redir.aspx?SURL=y44JoDKtWxPkUtTXoC_Nf05OEJxV51i0p6rjKn2DN1ghwInISALTCG0AYQBpAGwAdABvADoAUgBhAGcAaQBuAGkALgBWAGUAcgBtAGEAQAB1AHAAaABzAC4AdQBwAGUAbgBuAC4AZQBkAHUA&URL=mailto%3aRagini.Verma%40uphs.upenn.edu>
.
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From arokem at gmail.com  Wed May 31 20:50:53 2017
From: arokem at gmail.com (Ariel Rokem)
Date: Wed, 31 May 2017 17:50:53 -0700
Subject: [Neuroimaging] Fwd: [Escience_bbl] Postdoctoral researcher position
 available
In-Reply-To: <CAOmHqf54ooOiMqw-yK3tqa6bZL0=jG2ez=MC30QQG7_BqZ7bMQ@mail.gmail.com>
References: <CAOmHqf54ooOiMqw-yK3tqa6bZL0=jG2ez=MC30QQG7_BqZ7bMQ@mail.gmail.com>
Message-ID: <CA+X4w0xBNNuMq3AzkNkJpB4piVe+69yX=Qv70D0XfeRvwmMBug@mail.gmail.com>

With apologies for cross-posting, this is an excellent opportunity to work
on data-intensive human neuroscience.

Ariel


---------- Forwarded message ----------
From: Robin E. Brooks <rebrooks at uw.edu>
Date: Wed, May 31, 2017 at 4:10 PM
Subject: [Escience_bbl] Postdoctoral researcher position available
To: escience_bbl at u.washington.edu


Hi all,

Please see below for information on a new research opportunity!

Postdoctoral Researcher Position
University of Washington, Seattle
Labs of Bingni Brunton and Rajesh Rao

A position for a Postdoctoral Researcher is available immediately to study
neural correlates of naturalistic human behaviors; this postdoctoral
position is federally funded and will be co-mentored by Dr. Bing Brunton
and Dr. Raj Rao. The project focuses on analyzing long-term, task-free
human intracranial electrocorticography (ECoG) recordings acquired in
conjunction with video and audio monitoring. Our overall goals for the
project are  1) to develop computational algorithms to discover and predict
patterns in this large, multi-modal dataset; and 2) to uncover basic
computational principles underlying naturalistic human behavior.

The applicant should have a Ph.D. in Neuroscience, Psychology, Computer
Science, Applied Mathematics, Statistics or a related field. The ideal
candidate will have a very strong background in neuroscience as well as
data-intensive, computational methods. Experience and expertise in working
with large datasets (such as data in cognitive neuroscience, behavior
analysis, human neuroscience, neuroimaging, and electrophysiology) are
helpful. Excellent verbal and written communication skills are required, as
much of our work requires explaining complex technical concepts to
non-experts.

The postdoc will be joining a dynamic and interdisciplinary team of
researchers including data scientists and neuroscientists. The postdoc will
be involved in several interdisciplinary institutes and centers at
University of Washington, including the UW Institute for Neuroengineering,
the UW eScience Institute, and the Center for Sensorimotor Neural
Engineering.

Interested candidates should contact Bing Brunton (bbrunton at uw.edu) and
Rajesh Rao (rao at cs.washington.edu). Please include a short cover letter of
your particular interest in this position, your CV, and contact information
for 2--3 references.

Kind regards,

Robin Brooks
Communications Associate  |  eScience Institute
<http://escience.washington.edu/>
206.543.9674 <(206)%20543-9674> & rebrooks at uw.edu
Follow us on Twitter <https://twitter.com/uwescience>, Facebook
<https://www.facebook.com/uwescienceinstitute/> and YouTube
<https://www.youtube.com/channel/UCLKSeDZWDqBzKRfHTabg1lQ>!
University of Washington
3910 15th Ave NE, Campus Box 351570  | Seattle, WA  98195



_______________________________________________
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Escience_bbl at u.washington.edu
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