<div dir="ltr"><div><div><div>Hi Juan,<br><br></div>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. <br><br></div>Cheers,<br><br></div>-Morgan<br></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Nov 14, 2017 at 9:08 AM <<a href="mailto:neuroimaging-request@python.org">neuroimaging-request@python.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Neuroimaging mailing list submissions to<br>
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or, via email, send a message with subject or body 'help' to<br>
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When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Neuroimaging digest..."<br>
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<br>
Today's Topics:<br>
<br>
1. Re: New to coding, looking for ways to practice and improve<br>
(Ariel Rokem)<br>
2. Re: New to coding, looking for ways to practice and improve<br>
(Eleftherios Garyfallidis)<br>
3. Re: New to coding, looking for ways to practice and improve<br>
(Juan Jes?s Torre Tresols)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 13 Nov 2017 20:02:40 -0500<br>
From: Ariel Rokem <<a href="mailto:arokem@gmail.com" target="_blank">arokem@gmail.com</a>><br>
To: Neuroimaging analysis in Python <<a href="mailto:neuroimaging@python.org" target="_blank">neuroimaging@python.org</a>><br>
Subject: Re: [Neuroimaging] New to coding, looking for ways to<br>
practice and improve<br>
Message-ID:<br>
<CA+X4w0x+pb-C+sGML2LKr1n=WR_yVNAZ+gDh-zyck7e=-<a href="mailto:YGZjw@mail.gmail.com" target="_blank">YGZjw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello Juan,<br>
<br>
Brainhack is a good direction!<br>
<br>
On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker <<a href="mailto:kw401@cam.ac.uk" target="_blank">kw401@cam.ac.uk</a>> wrote:<br>
<br>
> Hi Juan,<br>
><br>
> I think your best bet is to join the Brainhack slack group:<br>
> <a href="https://brainhack-slack-invite.herokuapp.com" rel="noreferrer" target="_blank">https://brainhack-slack-invite.herokuapp.com</a>.<br>
><br>
> You can find out more about Brainhack here: <a href="http://www.brainhack.org/" rel="noreferrer" target="_blank">http://www.brainhack.org/</a> but<br>
> in brief we're a community of neuroimagers who want to improve the state of<br>
> the science by building new open tools that can be used and improved by<br>
> others :)<br>
><br>
> The different channels in the slack team are different projects, many of<br>
> which are written in python. I'd recommend writing a little introduction in<br>
> the general channel (like your intro here) and asking if there are any<br>
> projects currently looking for contributors.<br>
><br>
> Have fun!<br>
> Kirstie<br>
><br>
><br>
><br>
> On 12 November 2017 at 14:30, Juan Jes?s Torre Tresols <<br>
> <a href="mailto:juanjesustorre@gmail.com" target="_blank">juanjesustorre@gmail.com</a>> wrote:<br>
><br>
>> Hello, members of the Python neuroimaging community.<br>
>><br>
>> I'm a graduate student of neuropsychology/neuroscience with experience in<br>
>> magnetoencephalography (MEG) data collection and analysis.<br>
>><br>
>><br>
I will just add that for your interests and background you might want to<br>
check out the MNE project:<br>
<br>
<a href="https://www.martinos.org/mne/stable/index.html" rel="noreferrer" target="_blank">https://www.martinos.org/mne/stable/index.html</a><br>
<br>
If you are interested in finding a place to start contributing, the "easy"<br>
tag in their issues might be a good place to look for things you can start<br>
doing to get acquainted with the project:<br>
<br>
<a href="https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+</a><br>
is%3Aissue+label%3AEASY<br>
<br>
Best,<br>
<br>
Ariel<br>
<br>
<br>
> As I'm currently unemployed and looking for a PhD vacancy related to<br>
>> neuroimaging, I started to learn Python in order to improve my curriculum.<br>
>> Now that I have finished learning the basics of the language, I started<br>
>> looking for applications or projects to further develop my programming<br>
>> skills.<br>
>><br>
>> I would like to ask you for guidance, since I'm new to programming and I<br>
>> don't really know what can I do or cannot do with Python, or what type of<br>
>> personal goals I can set for myself in order to continue learning. I really<br>
>> enjoyed learning Python, and I would like to put it to use in something<br>
>> related to neuroimaging.<br>
>><br>
>> Thank you very much for your time,<br>
>><br>
>> Juan Jes?s Torre Tresols<br>
>><br>
>><br>
>> <<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>> Libre<br>
>> de virus. <a href="http://www.avast.com" rel="noreferrer" target="_blank">www.avast.com</a><br>
>> <<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>><br>
>> <#m_4529354199073085713_m_-4757697563001603764_m_5529805611569612612_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2><br>
>><br>
>> _______________________________________________<br>
>> Neuroimaging mailing list<br>
>> <a href="mailto:Neuroimaging@python.org" target="_blank">Neuroimaging@python.org</a><br>
>> <a href="https://mail.python.org/mailman/listinfo/neuroimaging" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><br>
>><br>
>><br>
><br>
><br>
> --<br>
> Kirstie Whitaker, PhD<br>
><br>
> Research Fellow, Alan Turing Institute<br>
> Research Associate, University of Cambridge<br>
><br>
> *Mailing Address*<br>
> Brain Mapping Unit<br>
> Department of Psychiatry<br>
> Sir William Hardy Building<br>
> Downing Street<br>
> Cambridge CB2 3EB<br>
><br>
> *Phone: *<a href="tel:+44%207583%20535307" value="+447583535307" target="_blank">+44 7583 535 307</a> <+44%207583%20535307><br>
> *Website:* <a href="https://whitakerlab.github.io" rel="noreferrer" target="_blank">https://whitakerlab.github.io</a><br>
> *Twitter:* @kirstie_j <<a href="https://twitter.com/kirstie_j" rel="noreferrer" target="_blank">https://twitter.com/kirstie_j</a>><br>
><br>
> _______________________________________________<br>
> Neuroimaging mailing list<br>
> <a href="mailto:Neuroimaging@python.org" target="_blank">Neuroimaging@python.org</a><br>
> <a href="https://mail.python.org/mailman/listinfo/neuroimaging" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><br>
><br>
><br>
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<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 14 Nov 2017 01:23:03 +0000<br>
From: Eleftherios Garyfallidis <<a href="mailto:elef@indiana.edu" target="_blank">elef@indiana.edu</a>><br>
To: Neuroimaging analysis in Python <<a href="mailto:neuroimaging@python.org" target="_blank">neuroimaging@python.org</a>><br>
Subject: Re: [Neuroimaging] New to coding, looking for ways to<br>
practice and improve<br>
Message-ID:<br>
<CAN6JmWNdHHKg7aJ+RD6-RL4QuK=<a href="mailto:ZRZiQfKjiwOcY8EPiYDeJrA@mail.gmail.com" target="_blank">ZRZiQfKjiwOcY8EPiYDeJrA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Juan,<br>
<br>
Also, make sure you don't stay at the basics of the Python language but<br>
look into data science related books such as Python for Data Analysis or<br>
similar. Get familiar with numpy, scipy and perhaps scikit-learn too. These<br>
can be very helpful in your future endeavors.<br>
<br>
And of course if want to get into computational anatomy areas we are here<br>
to help.<br>
<br>
All the best,<br>
Eleftherios<br>
<br>
<br>
On Mon, Nov 13, 2017 at 8:03 PM Ariel Rokem <<a href="mailto:arokem@gmail.com" target="_blank">arokem@gmail.com</a>> wrote:<br>
<br>
> Hello Juan,<br>
><br>
> Brainhack is a good direction!<br>
><br>
> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker <<a href="mailto:kw401@cam.ac.uk" target="_blank">kw401@cam.ac.uk</a>> wrote:<br>
><br>
>> Hi Juan,<br>
>><br>
>> I think your best bet is to join the Brainhack slack group:<br>
>> <a href="https://brainhack-slack-invite.herokuapp.com" rel="noreferrer" target="_blank">https://brainhack-slack-invite.herokuapp.com</a>.<br>
>><br>
>> You can find out more about Brainhack here: <a href="http://www.brainhack.org/" rel="noreferrer" target="_blank">http://www.brainhack.org/</a><br>
>> but in brief we're a community of neuroimagers who want to improve the<br>
>> state of the science by building new open tools that can be used and<br>
>> improved by others :)<br>
>><br>
>> The different channels in the slack team are different projects, many of<br>
>> which are written in python. I'd recommend writing a little introduction in<br>
>> the general channel (like your intro here) and asking if there are any<br>
>> projects currently looking for contributors.<br>
>><br>
>> Have fun!<br>
>> Kirstie<br>
>><br>
>><br>
>><br>
>> On 12 November 2017 at 14:30, Juan Jes?s Torre Tresols <<br>
>> <a href="mailto:juanjesustorre@gmail.com" target="_blank">juanjesustorre@gmail.com</a>> wrote:<br>
>><br>
>>> Hello, members of the Python neuroimaging community.<br>
>>><br>
>>> I'm a graduate student of neuropsychology/neuroscience with experience<br>
>>> in magnetoencephalography (MEG) data collection and analysis.<br>
>>><br>
>>><br>
> I will just add that for your interests and background you might want to<br>
> check out the MNE project:<br>
><br>
> <a href="https://www.martinos.org/mne/stable/index.html" rel="noreferrer" target="_blank">https://www.martinos.org/mne/stable/index.html</a><br>
><br>
> If you are interested in finding a place to start contributing, the "easy"<br>
> tag in their issues might be a good place to look for things you can start<br>
> doing to get acquainted with the project:<br>
><br>
><br>
> <a href="https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+is%3Aissue+label%3AEASY" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+is%3Aissue+label%3AEASY</a><br>
><br>
> Best,<br>
><br>
> Ariel<br>
><br>
><br>
>> As I'm currently unemployed and looking for a PhD vacancy related to<br>
>>> neuroimaging, I started to learn Python in order to improve my curriculum.<br>
>>> Now that I have finished learning the basics of the language, I started<br>
>>> looking for applications or projects to further develop my programming<br>
>>> skills.<br>
>>><br>
>>> I would like to ask you for guidance, since I'm new to programming and I<br>
>>> don't really know what can I do or cannot do with Python, or what type of<br>
>>> personal goals I can set for myself in order to continue learning. I really<br>
>>> enjoyed learning Python, and I would like to put it to use in something<br>
>>> related to neuroimaging.<br>
>>><br>
>>> Thank you very much for your time,<br>
>>><br>
>>> Juan Jes?s Torre Tresols<br>
>>><br>
>>><br>
>>> <<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>> Libre<br>
>>> de virus. <a href="http://www.avast.com" rel="noreferrer" target="_blank">www.avast.com</a><br>
>>> <<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>><br>
>>> <#m_301644474983820419_m_-1850395192785405891_m_4529354199073085713_m_-4757697563001603764_m_5529805611569612612_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2><br>
>>><br>
>>> _______________________________________________<br>
>>> Neuroimaging mailing list<br>
>>> <a href="mailto:Neuroimaging@python.org" target="_blank">Neuroimaging@python.org</a><br>
>>> <a href="https://mail.python.org/mailman/listinfo/neuroimaging" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><br>
>>><br>
>>><br>
>><br>
>><br>
>> --<br>
>> Kirstie Whitaker, PhD<br>
>><br>
>> Research Fellow, Alan Turing Institute<br>
>> Research Associate, University of Cambridge<br>
>><br>
>> *Mailing Address*<br>
>> Brain Mapping Unit<br>
>> Department of Psychiatry<br>
>> Sir William Hardy Building<br>
>> Downing Street<br>
>> Cambridge CB2 3EB<br>
>><br>
>> *Phone: *<a href="tel:+44%207583%20535307" value="+447583535307" target="_blank">+44 7583 535 307</a> <+44%207583%20535307><br>
>> *Website:* <a href="https://whitakerlab.github.io" rel="noreferrer" target="_blank">https://whitakerlab.github.io</a><br>
>> *Twitter:* @kirstie_j <<a href="https://twitter.com/kirstie_j" rel="noreferrer" target="_blank">https://twitter.com/kirstie_j</a>><br>
>><br>
>> _______________________________________________<br>
>> Neuroimaging mailing list<br>
>> <a href="mailto:Neuroimaging@python.org" target="_blank">Neuroimaging@python.org</a><br>
>> <a href="https://mail.python.org/mailman/listinfo/neuroimaging" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><br>
>><br>
>> _______________________________________________<br>
> Neuroimaging mailing list<br>
> <a href="mailto:Neuroimaging@python.org" target="_blank">Neuroimaging@python.org</a><br>
> <a href="https://mail.python.org/mailman/listinfo/neuroimaging" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><br>
><br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 14 Nov 2017 09:32:19 +0100<br>
From: Juan Jes?s Torre Tresols <<a href="mailto:juanjesustorre@gmail.com" target="_blank">juanjesustorre@gmail.com</a>><br>
To: Neuroimaging analysis in Python <<a href="mailto:neuroimaging@python.org" target="_blank">neuroimaging@python.org</a>><br>
Subject: Re: [Neuroimaging] New to coding, looking for ways to<br>
practice and improve<br>
Message-ID:<br>
<CA++OTEgcCh5NR9T_G51WTnYVRL7AN2VmE4YPbKbN15Qaj8K=<a href="mailto:tw@mail.gmail.com" target="_blank">tw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
Thank you very much for your advice! It's much appreciated. I already<br>
checked the brainhack and MNE projects, I'll sure have a look on that<br>
"easy" tagged requests soon!<br>
<br>
Also, thank you for suggesting frequently used toold and useful textbooks.<br>
I would like to get into computational anatomy too, where could I start?<br>
<br>
Thank you very much again,<br>
<br>
Juan<br>
<br>
<<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>><br>
Libre<br>
de virus. <a href="http://www.avast.com" rel="noreferrer" target="_blank">www.avast.com</a><br>
<<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>><br>
<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2><br>
<br>
On Tue, Nov 14, 2017 at 2:23 AM, Eleftherios Garyfallidis <<a href="mailto:elef@indiana.edu" target="_blank">elef@indiana.edu</a>><br>
wrote:<br>
<br>
> Hi Juan,<br>
><br>
> Also, make sure you don't stay at the basics of the Python language but<br>
> look into data science related books such as Python for Data Analysis or<br>
> similar. Get familiar with numpy, scipy and perhaps scikit-learn too. These<br>
> can be very helpful in your future endeavors.<br>
><br>
> And of course if want to get into computational anatomy areas we are here<br>
> to help.<br>
><br>
> All the best,<br>
> Eleftherios<br>
><br>
><br>
> On Mon, Nov 13, 2017 at 8:03 PM Ariel Rokem <<a href="mailto:arokem@gmail.com" target="_blank">arokem@gmail.com</a>> wrote:<br>
><br>
>> Hello Juan,<br>
>><br>
>> Brainhack is a good direction!<br>
>><br>
>> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker <<a href="mailto:kw401@cam.ac.uk" target="_blank">kw401@cam.ac.uk</a>><br>
>> wrote:<br>
>><br>
>>> Hi Juan,<br>
>>><br>
>>> I think your best bet is to join the Brainhack slack group:<br>
>>> <a href="https://brainhack-slack-invite.herokuapp.com" rel="noreferrer" target="_blank">https://brainhack-slack-invite.herokuapp.com</a>.<br>
>>><br>
>>> You can find out more about Brainhack here: <a href="http://www.brainhack.org/" rel="noreferrer" target="_blank">http://www.brainhack.org/</a><br>
>>> but in brief we're a community of neuroimagers who want to improve the<br>
>>> state of the science by building new open tools that can be used and<br>
>>> improved by others :)<br>
>>><br>
>>> The different channels in the slack team are different projects, many of<br>
>>> which are written in python. I'd recommend writing a little introduction in<br>
>>> the general channel (like your intro here) and asking if there are any<br>
>>> projects currently looking for contributors.<br>
>>><br>
>>> Have fun!<br>
>>> Kirstie<br>
>>><br>
>>><br>
>>><br>
>>> On 12 November 2017 at 14:30, Juan Jes?s Torre Tresols <<br>
>>> <a href="mailto:juanjesustorre@gmail.com" target="_blank">juanjesustorre@gmail.com</a>> wrote:<br>
>>><br>
>>>> Hello, members of the Python neuroimaging community.<br>
>>>><br>
>>>> I'm a graduate student of neuropsychology/neuroscience with experience<br>
>>>> in magnetoencephalography (MEG) data collection and analysis.<br>
>>>><br>
>>>><br>
>> I will just add that for your interests and background you might want to<br>
>> check out the MNE project:<br>
>><br>
>> <a href="https://www.martinos.org/mne/stable/index.html" rel="noreferrer" target="_blank">https://www.martinos.org/mne/stable/index.html</a><br>
>><br>
>> If you are interested in finding a place to start contributing, the<br>
>> "easy" tag in their issues might be a good place to look for things you can<br>
>> start doing to get acquainted with the project:<br>
>><br>
>> <a href="https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues?q=is%3Aopen+</a><br>
>> is%3Aissue+label%3AEASY<br>
>><br>
>> Best,<br>
>><br>
>> Ariel<br>
>><br>
>><br>
>>> As I'm currently unemployed and looking for a PhD vacancy related to<br>
>>>> neuroimaging, I started to learn Python in order to improve my curriculum.<br>
>>>> Now that I have finished learning the basics of the language, I started<br>
>>>> looking for applications or projects to further develop my programming<br>
>>>> skills.<br>
>>>><br>
>>>> I would like to ask you for guidance, since I'm new to programming and<br>
>>>> I don't really know what can I do or cannot do with Python, or what type of<br>
>>>> personal goals I can set for myself in order to continue learning. I really<br>
>>>> enjoyed learning Python, and I would like to put it to use in something<br>
>>>> related to neuroimaging.<br>
>>>><br>
>>>> Thank you very much for your time,<br>
>>>><br>
>>>> Juan Jes?s Torre Tresols<br>
>>>><br>
>>>><br>
>>>> <<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>> Libre<br>
>>>> de virus. <a href="http://www.avast.com" rel="noreferrer" target="_blank">www.avast.com</a><br>
>>>> <<a href="https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" rel="noreferrer" target="_blank">https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail</a>><br>
>>>> <#m_5356533663828081782_m_301644474983820419_m_-1850395192785405891_m_4529354199073085713_m_-4757697563001603764_m_5529805611569612612_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2><br>
>>>><br>
>>>> _______________________________________________<br>
>>>> Neuroimaging mailing list<br>
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>>>><br>
>>>><br>
>>><br>
>>><br>
>>> --<br>
>>> Kirstie Whitaker, PhD<br>
>>><br>
>>> Research Fellow, Alan Turing Institute<br>
>>> Research Associate, University of Cambridge<br>
>>><br>
>>> *Mailing Address*<br>
>>> Brain Mapping Unit<br>
>>> Department of Psychiatry<br>
>>> Sir William Hardy Building<br>
>>> Downing Street<br>
>>> Cambridge CB2 3EB<br>
>>><br>
>>> *Phone: *<a href="tel:+44%207583%20535307" value="+447583535307" target="_blank">+44 7583 535 307</a> <+44%207583%20535307><br>
>>> *Website:* <a href="https://whitakerlab.github.io" rel="noreferrer" target="_blank">https://whitakerlab.github.io</a><br>
>>> *Twitter:* @kirstie_j <<a href="https://twitter.com/kirstie_j" rel="noreferrer" target="_blank">https://twitter.com/kirstie_j</a>><br>
>>><br>
>>> _______________________________________________<br>
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>>><br>
>>> _______________________________________________<br>
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>><br>
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End of Neuroimaging Digest, Vol 30, Issue 8<br>
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