[Neuroimaging] Neuroimaging Digest, Vol 30, Issue 8
Morgan Hough
morgan.hough at gmail.com
Tue Nov 14 16:48:05 EST 2017
Hi Juan,
For the computational anatomy, you could certainly look at the key stages
of FreeSurfer's recon-all pipeline. Your going to want to know its output
well for MNE anyway but its more commonly used as a computational
neuroanatomy tool. Hope that helps.
Cheers,
-Morgan
On Tue, Nov 14, 2017 at 9:08 AM <neuroimaging-request at python.org> wrote:
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> Today's Topics:
>
> 1. Re: New to coding, looking for ways to practice and improve
> (Ariel Rokem)
> 2. Re: New to coding, looking for ways to practice and improve
> (Eleftherios Garyfallidis)
> 3. Re: New to coding, looking for ways to practice and improve
> (Juan Jes?s Torre Tresols)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Nov 2017 20:02:40 -0500
> From: Ariel Rokem <arokem at gmail.com>
> To: Neuroimaging analysis in Python <neuroimaging at python.org>
> Subject: Re: [Neuroimaging] New to coding, looking for ways to
> practice and improve
> Message-ID:
> <CA+X4w0x+pb-C+sGML2LKr1n=WR_yVNAZ+gDh-zyck7e=-
> YGZjw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Juan,
>
> Brainhack is a good direction!
>
> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker <kw401 at cam.ac.uk> wrote:
>
> > Hi Juan,
> >
> > I think your best bet is to join the Brainhack slack group:
> > https://brainhack-slack-invite.herokuapp.com.
> >
> > You can find out more about Brainhack here: http://www.brainhack.org/
> but
> > in brief we're a community of neuroimagers who want to improve the state
> of
> > the science by building new open tools that can be used and improved by
> > others :)
> >
> > The different channels in the slack team are different projects, many of
> > which are written in python. I'd recommend writing a little introduction
> in
> > the general channel (like your intro here) and asking if there are any
> > projects currently looking for contributors.
> >
> > Have fun!
> > Kirstie
> >
> >
> >
> > On 12 November 2017 at 14:30, Juan Jes?s Torre Tresols <
> > juanjesustorre at gmail.com> wrote:
> >
> >> Hello, members of the Python neuroimaging community.
> >>
> >> I'm a graduate student of neuropsychology/neuroscience with experience
> in
> >> magnetoencephalography (MEG) data collection and analysis.
> >>
> >>
> I will just add that for your interests and background you might want to
> check out the MNE project:
>
> https://www.martinos.org/mne/stable/index.html
>
> If you are interested in finding a place to start contributing, the "easy"
> tag in their issues might be a good place to look for things you can start
> doing to get acquainted with the project:
>
> https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+
> is%3Aissue+label%3AEASY
>
> Best,
>
> Ariel
>
>
> > As I'm currently unemployed and looking for a PhD vacancy related to
> >> neuroimaging, I started to learn Python in order to improve my
> curriculum.
> >> Now that I have finished learning the basics of the language, I started
> >> looking for applications or projects to further develop my programming
> >> skills.
> >>
> >> I would like to ask you for guidance, since I'm new to programming and I
> >> don't really know what can I do or cannot do with Python, or what type
> of
> >> personal goals I can set for myself in order to continue learning. I
> really
> >> enjoyed learning Python, and I would like to put it to use in something
> >> related to neuroimaging.
> >>
> >> Thank you very much for your time,
> >>
> >> Juan Jes?s Torre Tresols
> >>
> >>
> >> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> Libre
> >> de virus. www.avast.com
> >> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> >>
> <#m_4529354199073085713_m_-4757697563001603764_m_5529805611569612612_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >>
> >> _______________________________________________
> >> Neuroimaging mailing list
> >> Neuroimaging at python.org
> >> https://mail.python.org/mailman/listinfo/neuroimaging
> >>
> >>
> >
> >
> > --
> > Kirstie Whitaker, PhD
> >
> > Research Fellow, Alan Turing Institute
> > Research Associate, University of Cambridge
> >
> > *Mailing Address*
> > Brain Mapping Unit
> > Department of Psychiatry
> > Sir William Hardy Building
> > Downing Street
> > Cambridge CB2 3EB
> >
> > *Phone: *+44 7583 535 307 <+44%207583%20535307> <+44%207583%20535307>
> > *Website:* https://whitakerlab.github.io
> > *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> >
> >
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> ------------------------------
>
> Message: 2
> Date: Tue, 14 Nov 2017 01:23:03 +0000
> From: Eleftherios Garyfallidis <elef at indiana.edu>
> To: Neuroimaging analysis in Python <neuroimaging at python.org>
> Subject: Re: [Neuroimaging] New to coding, looking for ways to
> practice and improve
> Message-ID:
> <CAN6JmWNdHHKg7aJ+RD6-RL4QuK=
> ZRZiQfKjiwOcY8EPiYDeJrA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Juan,
>
> Also, make sure you don't stay at the basics of the Python language but
> look into data science related books such as Python for Data Analysis or
> similar. Get familiar with numpy, scipy and perhaps scikit-learn too. These
> can be very helpful in your future endeavors.
>
> And of course if want to get into computational anatomy areas we are here
> to help.
>
> All the best,
> Eleftherios
>
>
> On Mon, Nov 13, 2017 at 8:03 PM Ariel Rokem <arokem at gmail.com> wrote:
>
> > Hello Juan,
> >
> > Brainhack is a good direction!
> >
> > On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker <kw401 at cam.ac.uk>
> wrote:
> >
> >> Hi Juan,
> >>
> >> I think your best bet is to join the Brainhack slack group:
> >> https://brainhack-slack-invite.herokuapp.com.
> >>
> >> You can find out more about Brainhack here: http://www.brainhack.org/
> >> but in brief we're a community of neuroimagers who want to improve the
> >> state of the science by building new open tools that can be used and
> >> improved by others :)
> >>
> >> The different channels in the slack team are different projects, many of
> >> which are written in python. I'd recommend writing a little
> introduction in
> >> the general channel (like your intro here) and asking if there are any
> >> projects currently looking for contributors.
> >>
> >> Have fun!
> >> Kirstie
> >>
> >>
> >>
> >> On 12 November 2017 at 14:30, Juan Jes?s Torre Tresols <
> >> juanjesustorre at gmail.com> wrote:
> >>
> >>> Hello, members of the Python neuroimaging community.
> >>>
> >>> I'm a graduate student of neuropsychology/neuroscience with experience
> >>> in magnetoencephalography (MEG) data collection and analysis.
> >>>
> >>>
> > I will just add that for your interests and background you might want to
> > check out the MNE project:
> >
> > https://www.martinos.org/mne/stable/index.html
> >
> > If you are interested in finding a place to start contributing, the
> "easy"
> > tag in their issues might be a good place to look for things you can
> start
> > doing to get acquainted with the project:
> >
> >
> >
> https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+is%3Aissue+label%3AEASY
> >
> > Best,
> >
> > Ariel
> >
> >
> >> As I'm currently unemployed and looking for a PhD vacancy related to
> >>> neuroimaging, I started to learn Python in order to improve my
> curriculum.
> >>> Now that I have finished learning the basics of the language, I started
> >>> looking for applications or projects to further develop my programming
> >>> skills.
> >>>
> >>> I would like to ask you for guidance, since I'm new to programming and
> I
> >>> don't really know what can I do or cannot do with Python, or what type
> of
> >>> personal goals I can set for myself in order to continue learning. I
> really
> >>> enjoyed learning Python, and I would like to put it to use in something
> >>> related to neuroimaging.
> >>>
> >>> Thank you very much for your time,
> >>>
> >>> Juan Jes?s Torre Tresols
> >>>
> >>>
> >>> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> Libre
> >>> de virus. www.avast.com
> >>> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> >>>
> <#m_301644474983820419_m_-1850395192785405891_m_4529354199073085713_m_-4757697563001603764_m_5529805611569612612_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >>>
> >>> _______________________________________________
> >>> Neuroimaging mailing list
> >>> Neuroimaging at python.org
> >>> https://mail.python.org/mailman/listinfo/neuroimaging
> >>>
> >>>
> >>
> >>
> >> --
> >> Kirstie Whitaker, PhD
> >>
> >> Research Fellow, Alan Turing Institute
> >> Research Associate, University of Cambridge
> >>
> >> *Mailing Address*
> >> Brain Mapping Unit
> >> Department of Psychiatry
> >> Sir William Hardy Building
> >> Downing Street
> >> Cambridge CB2 3EB
> >>
> >> *Phone: *+44 7583 535 307 <+44%207583%20535307> <+44%207583%20535307>
> >> *Website:* https://whitakerlab.github.io
> >> *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
> >>
> >> _______________________________________________
> >> 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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> ------------------------------
>
> Message: 3
> Date: Tue, 14 Nov 2017 09:32:19 +0100
> From: Juan Jes?s Torre Tresols <juanjesustorre at gmail.com>
> To: Neuroimaging analysis in Python <neuroimaging at python.org>
> Subject: Re: [Neuroimaging] New to coding, looking for ways to
> practice and improve
> Message-ID:
> <CA++OTEgcCh5NR9T_G51WTnYVRL7AN2VmE4YPbKbN15Qaj8K=
> tw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> Thank you very much for your advice! It's much appreciated. I already
> checked the brainhack and MNE projects, I'll sure have a look on that
> "easy" tagged requests soon!
>
> Also, thank you for suggesting frequently used toold and useful textbooks.
> I would like to get into computational anatomy too, where could I start?
>
> Thank you very much again,
>
> Juan
>
> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> Libre
> de virus. www.avast.com
> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Tue, Nov 14, 2017 at 2:23 AM, Eleftherios Garyfallidis <
> elef at indiana.edu>
> wrote:
>
> > Hi Juan,
> >
> > Also, make sure you don't stay at the basics of the Python language but
> > look into data science related books such as Python for Data Analysis or
> > similar. Get familiar with numpy, scipy and perhaps scikit-learn too.
> These
> > can be very helpful in your future endeavors.
> >
> > And of course if want to get into computational anatomy areas we are here
> > to help.
> >
> > All the best,
> > Eleftherios
> >
> >
> > On Mon, Nov 13, 2017 at 8:03 PM Ariel Rokem <arokem at gmail.com> wrote:
> >
> >> Hello Juan,
> >>
> >> Brainhack is a good direction!
> >>
> >> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker <kw401 at cam.ac.uk>
> >> wrote:
> >>
> >>> Hi Juan,
> >>>
> >>> I think your best bet is to join the Brainhack slack group:
> >>> https://brainhack-slack-invite.herokuapp.com.
> >>>
> >>> You can find out more about Brainhack here: http://www.brainhack.org/
> >>> but in brief we're a community of neuroimagers who want to improve the
> >>> state of the science by building new open tools that can be used and
> >>> improved by others :)
> >>>
> >>> The different channels in the slack team are different projects, many
> of
> >>> which are written in python. I'd recommend writing a little
> introduction in
> >>> the general channel (like your intro here) and asking if there are any
> >>> projects currently looking for contributors.
> >>>
> >>> Have fun!
> >>> Kirstie
> >>>
> >>>
> >>>
> >>> On 12 November 2017 at 14:30, Juan Jes?s Torre Tresols <
> >>> juanjesustorre at gmail.com> wrote:
> >>>
> >>>> Hello, members of the Python neuroimaging community.
> >>>>
> >>>> I'm a graduate student of neuropsychology/neuroscience with experience
> >>>> in magnetoencephalography (MEG) data collection and analysis.
> >>>>
> >>>>
> >> I will just add that for your interests and background you might want to
> >> check out the MNE project:
> >>
> >> https://www.martinos.org/mne/stable/index.html
> >>
> >> If you are interested in finding a place to start contributing, the
> >> "easy" tag in their issues might be a good place to look for things you
> can
> >> start doing to get acquainted with the project:
> >>
> >> https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+
> >> is%3Aissue+label%3AEASY
> >>
> >> Best,
> >>
> >> Ariel
> >>
> >>
> >>> As I'm currently unemployed and looking for a PhD vacancy related to
> >>>> neuroimaging, I started to learn Python in order to improve my
> curriculum.
> >>>> Now that I have finished learning the basics of the language, I
> started
> >>>> looking for applications or projects to further develop my programming
> >>>> skills.
> >>>>
> >>>> I would like to ask you for guidance, since I'm new to programming and
> >>>> I don't really know what can I do or cannot do with Python, or what
> type of
> >>>> personal goals I can set for myself in order to continue learning. I
> really
> >>>> enjoyed learning Python, and I would like to put it to use in
> something
> >>>> related to neuroimaging.
> >>>>
> >>>> Thank you very much for your time,
> >>>>
> >>>> Juan Jes?s Torre Tresols
> >>>>
> >>>>
> >>>> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
> Libre
> >>>> de virus. www.avast.com
> >>>> <
> https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail
> >
> >>>>
> <#m_5356533663828081782_m_301644474983820419_m_-1850395192785405891_m_4529354199073085713_m_-4757697563001603764_m_5529805611569612612_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
> >>>>
> >>>> _______________________________________________
> >>>> Neuroimaging mailing list
> >>>> Neuroimaging at python.org
> >>>> https://mail.python.org/mailman/listinfo/neuroimaging
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> Kirstie Whitaker, PhD
> >>>
> >>> Research Fellow, Alan Turing Institute
> >>> Research Associate, University of Cambridge
> >>>
> >>> *Mailing Address*
> >>> Brain Mapping Unit
> >>> Department of Psychiatry
> >>> Sir William Hardy Building
> >>> Downing Street
> >>> Cambridge CB2 3EB
> >>>
> >>> *Phone: *+44 7583 535 307 <+44%207583%20535307> <+44%207583%20535307>
> >>> *Website:* https://whitakerlab.github.io
> >>> *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> >
> >
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>
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