[Neuroimaging] Neuroimaging Digest, Vol 11, Issue 21

Thu Apr 28 13:00:05 EDT 2016

Thank You Samuel St-Jean!
I will Try the steps you mentioned....

On Thu, Apr 28, 2016 at 9:30 PM, <neuroimaging-request at python.org> wrote:

> Send Neuroimaging mailing list submissions to
>         neuroimaging at python.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://mail.python.org/mailman/listinfo/neuroimaging
> or, via email, send a message with subject or body 'help' to
>         neuroimaging-request at python.org
>
> You can reach the person managing the list at
>         neuroimaging-owner at python.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Neuroimaging digest..."
>
>
> Today's Topics:
>
>    1. Re: Contribute to cortical surface parcellation
>       (Eleftherios Garyfallidis)
>    2. post-doc position at Indiana University (Cheng, Hu)
>    3. Regarding PIESNO Paper by Koay (Vivek Joshi)
>    4. Re: Regarding PIESNO Paper by Koay (Samuel St-Jean)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Apr 2016 17:24:23 +0000
> From: Eleftherios Garyfallidis <garyfallidis at gmail.com>
> To: Neuroimaging analysis in Python <neuroimaging at python.org>
> Subject: Re: [Neuroimaging] Contribute to cortical surface
>         parcellation
> Message-ID:
>         <CAN6JmWMnNGnoqjRy+qxkc=
> KqqPHo1F0jcnOMNZ1nuBNMEpjE7Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Brahim,
>
> Apart from the information that Ariel asked I would like to tell you that
> there is no problem adding your algorithm in DIPY. But it would be great if
> you could generate a probabilistic nifti files from our existing
> probabilistic tracking algorithms rather that requiring always FSL files.
> This would make your method available to much larger range of input
> methods. But let's go step by step. Please send us your reference paper if
> you have already something submitted.
>
> It is also important for us to know if you are willing to help maintaining
> your code and fixing bugs let's say for at least 2 years after your code is
> merged. Maintenance is time consuming and we need to be sure that you can
> help with that.
>
> Let us know if you have other questions.
>
> Best regards,
> Eleftherios
>
>
> On Wed, Apr 27, 2016 at 10:42 AM Brahim Belaoucha <
> brahim.belaoucha at inria.fr>
> wrote:
>
> > Good morning,
> > I am sending you this email to ask if it is possible to include my code
> > that uses the probabilistic tractography results to parcellate the
> cortical
> > surface using different metrics.
> > my code now uses the results of FSL proba ilistic tractography (.nii.gz
> > images).
> >
> >
> > --
> > ---
> > Sincerely
> > Brahim Belaoucha
> >
> > PhD Student
> > Athena Project Team
> > Inria Sophia Antipolis - M?diterran?e
> > http://www-sop.inria.fr/athena/
> > Phone: (+33) 4-9238-7557
> > [image: inr_logo_corpo_UK_coul.png]
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mail.python.org/pipermail/neuroimaging/attachments/20160427/b2e61289/attachment-0001.html
> >
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: inr_logo_corpo_UK_coul.png
> Type: image/png
> Size: 6535 bytes
> Desc: not available
> URL: <
> http://mail.python.org/pipermail/neuroimaging/attachments/20160427/b2e61289/attachment-0001.png
> >
>
> ------------------------------
>
> Message: 2
> Date: Wed, 27 Apr 2016 20:06:51 +0000
> From: "Cheng, Hu" <hucheng at indiana.edu>
> To: "neuroimaging at python.org" <neuroimaging at python.org>
> Subject: [Neuroimaging] post-doc position at Indiana University
> Message-ID:
>         <54bc58c54cbb42138fb408d133159baa at in-cci-exch08.ads.iu.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
> We are seeking a motivated individual to work on the methodology
> development in neuroimaging as a post-doc/research scientist. The position
> starts in July 2016. The description of the position is attached.
>
> Hu Cheng, Ph.D., DABMP
> MRI Physicist, Imaging Research Facility
> Department of Psychological and Brain Sciences
> Adjunct Professor, Department of Physics
> Indiana University
> Bloomington, IN 47405
> Tel. 812-856-2518
> Fax. 812-855-4691
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mail.python.org/pipermail/neuroimaging/attachments/20160427/b97bb6ec/attachment-0001.html
> >
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Postdoctoral position in Neuroimaging.docx
> Type:
> application/vnd.openxmlformats-officedocument.wordprocessingml.document
> Size: 14895 bytes
> Desc: Postdoctoral position in Neuroimaging.docx
> URL: <
> http://mail.python.org/pipermail/neuroimaging/attachments/20160427/b97bb6ec/attachment-0001.docx
> >
>
> ------------------------------
>
> Message: 3
> Date: Thu, 28 Apr 2016 13:14:33 +0530
> From: Vivek Joshi <vivekjoshi1894 at gmail.com>
> To: neuroimaging at python.org
> Subject: [Neuroimaging] Regarding PIESNO Paper by Koay
> Message-ID:
>         <CAMYkJfvYiTCN0dsbiWmkFCu4Ggq6egkfuGSxdJzu75Es_xKJ=
> A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Respected Sir,
>                       My name is Vivek Joshi and i am doing a project on
> PIESNO by Koay for my final year project. We implemented the PIESNO code in
> python. But our Professor is asking us to identify the noise (whether
> rician or gaussian) present in mri images. So it would help me if you have
> any idea on how to identify noise. Please think about it.
>
> THANK YOU!!
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mail.python.org/pipermail/neuroimaging/attachments/20160428/c6843c36/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 4
> Date: Thu, 28 Apr 2016 13:36:06 +0200
> From: Samuel St-Jean <stjeansam at gmail.com>
> To: Neuroimaging analysis in Python <neuroimaging at python.org>
> Subject: Re: [Neuroimaging] Regarding PIESNO Paper by Koay
> Message-ID:
>         <
> CAKADGuqbvubeL+BtkXeLuBB-7YLtz3fn1wxi2MOB59fi6uAhhA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> As a first point, piesno actually works only (based on the math) for rician
> or non central chi distributed noise (which is what is commonly found in
> magnitude images in MRI) and correct for that case to get back an
> estimation of the standard deviation based on a single gaussian
> distribution. You could have a look at [1] to get a feeling of the various
> noise distribution encountered in most cases, as the gaussian case would
> only apply if you also collect phase data I'd say (or do fancy
> pre-processing scanner side, which is not commonly done by everyone).
>
> Anyway, to go more toward your question, you can have at [2] which gives
> method to estimate the number of coils of the acquisition. Although these
> require knowledge in the type of acquisition you have, it does lay some
> groundwork for ideas on how to estimate the noise from any acquisition. I
> also tried to implement the method of [3] (probably have some code lying
> around if I look hard enough if you would want it) but found the estimation
> to not be inline with my simulations (could be also my quick
> implementation, I had nothing to compare against).
>
> Talking about implementation, if you want to validate/add features to it,
> there is alos another piesno implementation over here :
> https://github.com/nipy/dipy/blob/master/dipy/denoise/noise_estimate.py
>
> This was validated against the original closed source code, but as you can
> see I used the precomputed tables from the article. If you also have the
> original equations implemented instead of the precomputed value it would be
> a great addition (since it requires 1D optimisation, I though it would be
> too slow to compute it each time, so you might also want to use these
> tables instead in that case.)
>
> Anyway, if you need more help feel free to ask back.
>
> Samuel
>
> [1] Dietrich et al. 2008 Measurement of signal-to-noise ratios in MR
> images: Influence of multichannel coils, parallel imaging, and
> reconstruction filters
> [2] Aja-Fern?ndez, S., Vegas-S?nchez-Ferrero, G., Trist?n-Vega, A., 2014.
> Noise estimation in parallel MRI: GRAPPA and SENSE. Magnetic resonance
> imaging 32, 281?90.
> [3] Veraart et al. 2013 Comprehensive framework for accurate diffusion MRI
> parameter estimation
>
> 2016-04-28 9:44 GMT+02:00 Vivek Joshi <vivekjoshi1894 at gmail.com>:
>
> > Respected Sir,
> >                       My name is Vivek Joshi and i am doing a project on
> > PIESNO by Koay for my final year project. We implemented the PIESNO code
> in
> > python. But our Professor is asking us to identify the noise (whether
> > rician or gaussian) present in mri images. So it would help me if you
> have
> > any idea on how to identify noise. Please think about it.
> >
> > THANK YOU!!
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mail.python.org/pipermail/neuroimaging/attachments/20160428/967f4b71/attachment-0001.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>
> ------------------------------
>
> End of Neuroimaging Digest, Vol 11, Issue 21
> ********************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20160428/211a6f12/attachment.html>