From arokem at gmail.com Fri Nov 3 09:28:05 2017 From: arokem at gmail.com (Ariel Rokem) Date: Fri, 3 Nov 2017 06:28:05 -0700 Subject: [Neuroimaging] Neuroinformatics job opening, Brigham and Women's Hospital, Boston, MA Message-ID: >From Ofer Pasternak: The research specialist will join the Psychiatry Neuroimaging Laboratory (PNL), an active neuroimaging research group at Brigham and Women?s Hospital focused on understanding brain abnormalities and their role in neuropsychiatric disorders using state-of-the-art neuroimaging techniques. The team consists of a dynamic, interdisciplinary and international group of neuroscience researchers, physicians, computer scientists and students, all of whom are investigating the role of brain abnormalities in a variety of disorders including schizophrenia, post-traumatic stress disorder, traumatic brain injury, chronic traumatic encephalopathy, and attention-deficit hyperactivity disorder. This research group is also actively developing new technology to characterize brain structure and function, which has led to the design of state-of-the-art image analysis pipelines capable of robustly processing hundreds of neuroimaging datasets. The role of the research specialist will be to maintain and enhance existing image processing pipelines used at the PNL, and to develop new pipelines based on the latest research on image processing with an emphasis on version tracking, data provenance, and high performance computing. The group has been continuously funded through grant support from the National Institute of Mental Health, the National Institute of Neurological Disorders and Stroke, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the Department of Defense, the Veterans Medical Administration, and a variety of other public and private foundations. https://partners.taleo.net/ careersection/jobdetail.ftl?job=3050462&lang=en#.WfDstC-W33w.email -------------- next part -------------- An HTML attachment was scrubbed... URL: From lucian.dimitrievici at gmail.com Sat Nov 4 07:42:59 2017 From: lucian.dimitrievici at gmail.com (Lucian Dimitrievici) Date: Sat, 4 Nov 2017 13:42:59 +0200 Subject: [Neuroimaging] Request :) Message-ID: Hello, my name in Lucian Traian Dimitrievici, I am a PHD student in the Physics and Environmental engineering "Dunarea de Jos", Galati. My research concerns medical image processing and segmentation Is it possible to run script reconst_dki.py with another set of dates? I have dicom files and I dont where are they read or import -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Mon Nov 6 10:16:41 2017 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Mon, 6 Nov 2017 16:16:41 +0100 Subject: [Neuroimaging] Request :) In-Reply-To: References: Message-ID: Hi Lucian, the example uses the read_cfin_dwi() method to read the data, which is defined in data/fetcher.py, and loads the CFIN multi b-value diffusion images and the corresponding gradient tables. The data are downloaded and stored locally as you run the file. If you want to read another set of diffusion images, you will need to modify the example to allow some custom input parameters, and use the io/gradients.py:read_bvals_bvecs method to load the b-values and b-vectors, core/gradients.py:gradient_table to load the gradient table, and finally the nibabel's loadsave.py:load function to load the DWI images. Take into account that nibabel's support for DICOM is limited [1]. In dipy, and neuroimaging in general, it is more common to use NIfTI. HTH, JON HAITZ [1] http://nipy.org/nibabel/ -- On 4 November 2017 at 12:42, Lucian Dimitrievici wrote: > > Hello, my name in Lucian Traian Dimitrievici, I am a PHD student in the Physics and Environmental engineering "Dunarea de Jos", Galati. > My research concerns medical image processing and segmentation > Is it possible to run script reconst_dki.py with another set of dates? I have dicom files and I dont where are they read or import > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > From arokem at gmail.com Mon Nov 6 17:44:29 2017 From: arokem at gmail.com (Ariel Rokem) Date: Mon, 6 Nov 2017 22:44:29 +0000 Subject: [Neuroimaging] Fwd: [Uwin_news] Neuroengineering postdoctoral fellowships at the University of Washington In-Reply-To: References: Message-ID: Dear Nipy-ers, See below for an extraordinary post-doc opportunity at the University of Washington (Seattle). Feel free to email me off-list if you have questions about the fellowship, or about research opportunities at UW. Cheers, Ariel ---------- Forwarded message ---------- From: Alison Mehravari Date: Mon, Nov 6, 2017 at 10:32 PM Subject: [Uwin_news] Neuroengineering postdoctoral fellowships at the University of Washington To: "uwin_news at uw.edu" We invite applications for the *Washington Research Foundation Innovation Postdoctoral Fellowships in Neuroengineering* at the University of Washington in Seattle. These fellowships are offered through the UW Institute for Neuroengineering (UWIN), which links advances in biology, computing, devices, data science, and computational neuroscience to solve some of today?s greatest scientific challenges about neural system function. These highly selective fellowships fund research in computational and engineering approaches to neuroscience; joint mentoring between faculty in different disciplines is strongly encouraged. The fellowships provide two years of funding including a $65,000 annual salary and a $25,000 research stipend. Applications are due by Tuesday, January 16, 2018. Please see http://uwin.washington.edu/post-docs/ for more information. ------------------------- *Alison Mehravari*, Ph.D*. * Assistant Director of Operations University of Washington Institute for Neuroengineering Air Force Center of Excellence: Nature Inspired Flight Technologies and Ideas Daniel Lab, Department of Biology University of Washington Box 351800, Seattle, WA 98195 amehrava at uw.edu, 206-543-7335 <(206)%20543-7335> _______________________________________________ Uwin_news mailing list Uwin_news at u.washington.edu http://mailman11.u.washington.edu/mailman/listinfo/uwin_news -------------- next part -------------- An HTML attachment was scrubbed... URL: From eran_dayan at med.unc.edu Wed Nov 8 21:06:43 2017 From: eran_dayan at med.unc.edu (Dayan, Eran) Date: Thu, 9 Nov 2017 02:06:43 +0000 Subject: [Neuroimaging] Postdoctoral Research Associate in neuroimaging/data science In-Reply-To: References: Message-ID: A Postdoctoral Research Associate position is immediately open to work with the Network Neuroscience lab (dayanlab.web.unc.edu) at the Biomedical Research Imaging Center, University of North Carolina at Chapel Hill. The position is open to accomplished and highly motivated candidates, with an interest in neuroimaging and clinical neuroscience. The lab focuses on fundamental questions relating to brain network organization in health and disease, while aiming to develop methods and tools that could eventually be used in the clinic. The Postdoctoral Research Associate will develop and test a dimensional analysis framework for neurological dysfunction, using rich existing multimodal neuroimaging datasets obtained from patients and age-matched controls. Ample training and career development opportunities will be provided, as well as opportunities to collaborate with other groups at UNC. Ph.D. or an MD/Ph.D. in Neuroscience, Computer Science, Biomedical Engineering, Physics, Psychology or other related fields is required. Excellent quantitative background, relevant programming experience (MATLAB, Python or R), experience analyzing functional and/or structural MRI data and a track record of first-author publications in peer-reviewed journals are required. Experience in machine learning (particularly deep learning) would be advantageous. To apply, please visit https://unc.peopleadmin.com/postings/107413 and click the Apply for this Job link/button. For informal inquiries about the position, please email Dr. Eran Dayan at: eran_dayan at med.unc.edu The University of North Carolina at Chapel Hill is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to age, color, disability, gender, gender expression, gender identity, genetic information, race, national origin -------------- next part -------------- An HTML attachment was scrubbed... URL: From juanjesustorre at gmail.com Sun Nov 12 09:30:19 2017 From: juanjesustorre at gmail.com (=?UTF-8?Q?Juan_Jes=C3=BAs_Torre_Tresols?=) Date: Sun, 12 Nov 2017 15:30:19 +0100 Subject: [Neuroimaging] New to coding, looking for ways to practice and improve Message-ID: Hello, members of the Python neuroimaging community. I'm a graduate student of neuropsychology/neuroscience with experience in magnetoencephalography (MEG) data collection and analysis. 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 Libre de virus. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -------------- next part -------------- An HTML attachment was scrubbed... URL: From kw401 at cam.ac.uk Mon Nov 13 04:00:44 2017 From: kw401 at cam.ac.uk (Kirstie Whitaker) Date: Mon, 13 Nov 2017 09:00:44 +0000 Subject: [Neuroimaging] New to coding, looking for ways to practice and improve In-Reply-To: References: Message-ID: 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. > > 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 > > > Libre > de virus. www.avast.com > > <#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 *Website:* https://whitakerlab.github.io *Twitter:* @kirstie_j -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Mon Nov 13 20:02:40 2017 From: arokem at gmail.com (Ariel Rokem) Date: Mon, 13 Nov 2017 20:02:40 -0500 Subject: [Neuroimaging] New to coding, looking for ways to practice and improve In-Reply-To: References: Message-ID: Hello Juan, Brainhack is a good direction! On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker 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 >> >> >> Libre >> de virus. www.avast.com >> >> <#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> > *Website:* https://whitakerlab.github.io > *Twitter:* @kirstie_j > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Mon Nov 13 20:23:03 2017 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Tue, 14 Nov 2017 01:23:03 +0000 Subject: [Neuroimaging] New to coding, looking for ways to practice and improve In-Reply-To: References: Message-ID: 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 wrote: > Hello Juan, > > Brainhack is a good direction! > > On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker 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 >>> >>> >>> Libre >>> de virus. www.avast.com >>> >>> <#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> >> *Website:* https://whitakerlab.github.io >> *Twitter:* @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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From juanjesustorre at gmail.com Tue Nov 14 03:32:19 2017 From: juanjesustorre at gmail.com (=?UTF-8?Q?Juan_Jes=C3=BAs_Torre_Tresols?=) Date: Tue, 14 Nov 2017 09:32:19 +0100 Subject: [Neuroimaging] New to coding, looking for ways to practice and improve In-Reply-To: References: Message-ID: 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 Libre de virus. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Tue, Nov 14, 2017 at 2:23 AM, Eleftherios Garyfallidis 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 wrote: > >> Hello Juan, >> >> Brainhack is a good direction! >> >> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker >> 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 >>>> >>>> >>>> Libre >>>> de virus. www.avast.com >>>> >>>> <#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> >>> *Website:* https://whitakerlab.github.io >>> *Twitter:* @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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Tue Nov 14 14:52:44 2017 From: arokem at gmail.com (Ariel Rokem) Date: Tue, 14 Nov 2017 11:52:44 -0800 Subject: [Neuroimaging] New to coding, looking for ways to practice and improve In-Reply-To: References: Message-ID: On Tue, Nov 14, 2017 at 12:32 AM, Juan Jes?s Torre Tresols < juanjesustorre at gmail.com> wrote: > 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? > > I think the Eleftherios meant to point you to the Dipy project: http://nipy.org/dipy/ and https://github.com/nipy/dipy > Thank you very much again, > > Juan > > > Libre > de virus. www.avast.com > > <#m_-764201458135164681_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 wrote: >> >>> Hello Juan, >>> >>> Brainhack is a good direction! >>> >>> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker >>> 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+i >>> s%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 >>>>> >>>>> >>>>> Libre >>>>> de virus. www.avast.com >>>>> >>>>> <#m_-764201458135164681_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> >>>> *Website:* https://whitakerlab.github.io >>>> *Twitter:* @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 >> >> > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From morgan.hough at gmail.com Tue Nov 14 16:48:05 2017 From: morgan.hough at gmail.com (Morgan Hough) Date: Tue, 14 Nov 2017 21:48:05 +0000 Subject: [Neuroimaging] Neuroimaging Digest, Vol 30, Issue 8 In-Reply-To: References: Message-ID: 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 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: 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 > To: Neuroimaging analysis in Python > Subject: Re: [Neuroimaging] New to coding, looking for ways to > practice and improve > Message-ID: > 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 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 > > > > _______________________________________________ > > 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/20171113/f4482073/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Tue, 14 Nov 2017 01:23:03 +0000 > From: Eleftherios Garyfallidis > To: Neuroimaging analysis in Python > Subject: Re: [Neuroimaging] New to coding, looking for ways to > practice and improve > Message-ID: > 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 wrote: > > > Hello Juan, > > > > Brainhack is a good direction! > > > > On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker > 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 > >> > >> _______________________________________________ > >> 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 > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mail.python.org/pipermail/neuroimaging/attachments/20171114/b9594a6d/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Tue, 14 Nov 2017 09:32:19 +0100 > From: Juan Jes?s Torre Tresols > To: Neuroimaging analysis in Python > Subject: Re: [Neuroimaging] New to coding, looking for ways to > practice and improve > Message-ID: > 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 wrote: > > > >> Hello Juan, > >> > >> Brainhack is a good direction! > >> > >> On Mon, Nov 13, 2017 at 4:00 AM, Kirstie Whitaker > >> 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 > >>> > >>> _______________________________________________ > >>> 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 > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mail.python.org/pipermail/neuroimaging/attachments/20171114/5a2c39de/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 30, Issue 8 > ******************************************* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Fri Nov 17 11:19:52 2017 From: arokem at gmail.com (Ariel Rokem) Date: Fri, 17 Nov 2017 08:19:52 -0800 Subject: [Neuroimaging] ANN: Cloudknot 0.1 Message-ID: Hi everyone, Not a neuroimaging-specific tool, but might still be of interest to folks on this list: we are happy to announce the first release of *Cloudknot*, a software library that makes it easy to run your existing Python code at scale using AWS Batch. Documentation is here: https://richford.github.io/cloudknot/ The source code is available on Github: https://github.com/ric hford/cloudknot And there are few example use-cases (including analysis of MRI data!) here: https://github.com/richford/cloudknot/tree/master/examples To use it install with `pip install cloudknot`. A minimal example looks like this: ``` import cloudknot as ck def my_awesome_func(b): """Here is a function I want to run on AWS Batch""" # Always import dependencies within the function import numpy as np x = np.random.normal(0, b, 1024) A = np.random.normal(0, b, (1024, 1024)) return np.dot(A, x) # Create a `Knot`, the primary object in cloudknot (docs ) knot = ck.Knot(name='my_awesome_func', func=my_awesome_func) # Submit 20 jobs (each one will run on AWS batch and then send the results back here) result_futures = knot.map(range(1, 20)) ``` We welcome any feedback you have! Cheers, Ariel -------------- next part -------------- An HTML attachment was scrubbed... URL: From krzysztof.gorgolewski at gmail.com Fri Nov 17 11:31:07 2017 From: krzysztof.gorgolewski at gmail.com (Chris Gorgolewski) Date: Fri, 17 Nov 2017 08:31:07 -0800 Subject: [Neuroimaging] ANN: Cloudknot 0.1 In-Reply-To: References: Message-ID: Sounds super cool! Best, Chris On Nov 17, 2017 8:20 AM, "Ariel Rokem" wrote: > Hi everyone, > > Not a neuroimaging-specific tool, but might still be of interest to folks > on this list: we are happy to announce the first release of *Cloudknot*, > a software library that makes it easy to run your existing Python code at > scale using AWS Batch. > > Documentation is here: https://richford.github.io/cloudknot/ > > The source code is available on Github: https://github.com/ric > hford/cloudknot > > And there are few example use-cases (including analysis of MRI data!) > here: https://github.com/richford/cloudknot/tree/master/examples > > To use it install with `pip install cloudknot`. A minimal example looks > like this: > > ``` > import cloudknot as ck > > def my_awesome_func(b): > """Here is a function I want to run on AWS Batch""" > # Always import dependencies within the function > import numpy as np > > x = np.random.normal(0, b, 1024) > A = np.random.normal(0, b, (1024, 1024)) > > return np.dot(A, x) > > # Create a `Knot`, the primary object in cloudknot (docs > ) > knot = ck.Knot(name='my_awesome_func', func=my_awesome_func) > > # Submit 20 jobs (each one will run on AWS batch and then send the results > back here) > result_futures = knot.map(range(1, 20)) > ``` > > We welcome any feedback you have! > > Cheers, > > Ariel > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From albayenes at gmail.com Sat Nov 18 13:19:09 2017 From: albayenes at gmail.com (=?UTF-8?B?RW5lcyBBbGJheSAtINij2YbYsyDYp9mE2KjYp9mJ?=) Date: Sat, 18 Nov 2017 21:19:09 +0300 Subject: [Neuroimaging] Registration HARDI data to standard space Message-ID: Hi all, I want to make group analysis in diffusion data and I want to register my difusion data to same space but I could not figure out, how to register my raw HARDI diffusion data to standard space. For example, I think that first of all, for all subjects, I have to register b0 of each subject to T1 of each subject. After, register b0 in T1 to standard MNI space. At the end, apply same transformation pattern for all other diffusion direction images (there are 64 more direction other than b0). But I am not sure whether this is a correct solution or not. Also, I could not find the way to do this in dipy. Is my suggestion is meanigful or not and is there any way to do this? -- Enes Albay -------------- next part -------------- An HTML attachment was scrubbed... URL: From neon.taylor at gmail.com Wed Nov 22 12:11:45 2017 From: neon.taylor at gmail.com (P Taylor) Date: Wed, 22 Nov 2017 12:11:45 -0500 Subject: [Neuroimaging] Job opening: postdoc in AFNI group of NIH Message-ID: Hello- The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc, particularly someone with C and/or C++ experience, with Python and OpenGL skills also being quite useful. If you like problem solving and working with a fun group of people, then check out the attached advertisement for details. (And please feel free to forward on.) --pt -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Postdoc_In_AFNI_Group.pdf Type: application/pdf Size: 63846 bytes Desc: not available URL: From garyfallidis at gmail.com Wed Nov 22 14:34:49 2017 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Wed, 22 Nov 2017 19:34:49 +0000 Subject: [Neuroimaging] ANN: DIPY 0.13.0 release Message-ID: Hello all, We are happy to announce a new public release of Diffusion Imaging in Python (DIPY). This is mostly a maintenance release with extra fixes, speedups and minor changes of dependencies. *DIPY 0.13 (Tuesday, 24 October 2017)* This release received contributions from 13 developers (the full release notes are at: http://nipy.org/dipy/release0.13.html) *Highlights of this release include:* - Faster local PCA implementation. - Fixed different issues with OpenMP and Windows / OSX. - Replacement of cvxopt by cvxpy. - Replacement of Pytables by h5py. - Updated API to support latest numpy version (1.14). - New user interfaces for visualization. - Large documentation update. To upgrade, run the following command in your terminal: *pip install --upgrade dipy* or *conda install -c conda-forge dipy* For any questions go to http://dipy.org, or send an e-mail to neuroimaging at python.org We also have an instant messaging service and chat room available at https://gitter.im/nipy/dipy Expect mad features in release 0.14 (Jan 2018)! On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro http://dipy.org/developers.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From effigies at bu.edu Wed Nov 22 22:18:02 2017 From: effigies at bu.edu (Christopher Markiewicz) Date: Wed, 22 Nov 2017 22:18:02 -0500 Subject: [Neuroimaging] ANN: Nibabel release 2.2.1 Message-ID: Hi all, Just a quick announcement that nibabel has had a bugfix release, tagged 2.2.1. This release is largely motivated by 2.2.0 being unable to be included in standalone apps. This release should be safe to use with pyinstaller, py2app, or similar tools. Also, the built-in viewer was mislabeling left and right sides, so that's been fixed as well. As always, thanks to contributors, reviewers and users. Zenodo hasn't updated yet, but I'll update the release ( https://github.com/nipy/nibabel/releases/tag/2.2.1) with a DOI when it's assigned. The full Changelog follows: Bug fixes --------- * Set L/R labels in orthoview correctly (pr/564) (CM) * Defer use of ufunc / memmap test - allows "freezing" (pr/572) (MB, reviewed by Satra Ghosh) * Fix doctest failures with pre-release numpy (pr/582) (MB, reviewed by CM) Maintenance ----------- * Update documentation around NIfTI qform/sform codes (pr/576) (Paul McCarthy, reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by Paul McCarthy) * Skip precision test on macOS, newer numpy (pr/583) (MB, reviewed by CM) * Simplify AppVeyor script, removing conda (pr/584) (MB, reviewed by CM) Chris Markiewicz -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Thu Nov 23 03:15:38 2017 From: matthew.brett at gmail.com (Matthew Brett) Date: Thu, 23 Nov 2017 08:15:38 +0000 Subject: [Neuroimaging] ANN: Nibabel release 2.2.1 In-Reply-To: References: Message-ID: Hi Chris, On Thu, Nov 23, 2017 at 3:18 AM, Christopher Markiewicz wrote: > Hi all, > > Just a quick announcement that nibabel has had a bugfix release, tagged > 2.2.1. > > This release is largely motivated by 2.2.0 being unable to be included in > standalone apps. This release should be safe to use with pyinstaller, > py2app, or similar tools. Also, the built-in viewer was mislabeling left and > right sides, so that's been fixed as well. > > As always, thanks to contributors, reviewers and users. > > Zenodo hasn't updated yet, but I'll update the release > (https://github.com/nipy/nibabel/releases/tag/2.2.1) with a DOI when it's > assigned. > > > The full Changelog follows: > > Bug fixes > --------- > > * Set L/R labels in orthoview correctly (pr/564) (CM) > * Defer use of ufunc / memmap test - allows "freezing" (pr/572) (MB, > reviewed > by Satra Ghosh) > * Fix doctest failures with pre-release numpy (pr/582) (MB, reviewed by CM) > > Maintenance > ----------- > > * Update documentation around NIfTI qform/sform codes (pr/576) (Paul > McCarthy, > reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by Paul McCarthy) > * Skip precision test on macOS, newer numpy (pr/583) (MB, reviewed by CM) > * Simplify AppVeyor script, removing conda (pr/584) (MB, reviewed by CM) Great - thanks again for taking care of the release. Cheers, Matthew From bertrand.thirion at inria.fr Thu Nov 23 17:10:29 2017 From: bertrand.thirion at inria.fr (bthirion) Date: Thu, 23 Nov 2017 23:10:29 +0100 Subject: [Neuroimaging] Fwd: TR: Permanent position in high-resolution functional MRI at NeuroSpin In-Reply-To: <04b201d3643b$a15e0d60$e41a2820$@gmail.com> References: <04b201d3643b$a15e0d60$e41a2820$@gmail.com> Message-ID: *Permanent position in high-resolution human functional MRI at NeuroSpin* NeuroSpin, France?s research center for innovation in brain imaging technologies, is opening a*permanent position for a research scientist in high-resolution human functional MRI*. This is a pure research position, without any teaching requirement. We are looking for an experienced principal investigator. Both junior and senior candidates are welcome, and the salary will be modulated according to experience. Candidates should have a dual-track record: (1) a proven capacity to develop methods that push the spatial resolution of functional MRIand relate it to its anatomical substrate. (2) a strong publication record in any domain of cognitive neuroscience, either fundamental or clinical. Past experience could include one or more of the following: * fMRI sequence development, reconstruction and post-processing methods * Detailed fMRI mapping of individual subjects * High-resolution visualization of cortical maps or cortical columns * Determination of cortical codes (e.g. tuning curves, coding schemes?) * fMRI dissection of the functional role of cortical layers * Comparison of fMRI signals with intracranial and/or single-cell recordings * Relation of fMRI signals to anatomical and diffusion signals. Candidates are expected to develop their own research program using the 7 T and 11.7 T human magnetsavailable at NeuroSpin, while collaborating with the existing in-house teams. They will benefit from a dynamic scientific environment including scientists and support groups already working in all aspects of functional, anatomical and diffusion MRI as well as spectroscopy, from coil design to MR sequence development and reconstruction. The 7 T magnet is a state-of-the-art Siemens magnet, upgraded in early 2018 with the novel connectome whole-body gradient set running at 100mT/m, and fully equipped with visual, auditory, and eye-tracking devices. The 11.7 T is a world-premiere that will be up to field in late 2018, initially devoted to animal experiments, and seeking approval for human experiments around 2020-2021. Please send your letter of intention (1-2 pages), CV, and letters of recommendation, before December 31^st 2017, to Maryline Hevin, assistant to the director: maryline.hevin at cea.fr ?See also: http://team.inria.fr/parietal/files/2017/11/Permanent-position-in-high-resolution-fMRI-at-NeuroSpin.pdf -------------- next part -------------- An HTML attachment was scrubbed... URL: From saqibqamar25 at gmail.com Mon Nov 27 01:52:42 2017 From: saqibqamar25 at gmail.com (Saqib Qamar) Date: Mon, 27 Nov 2017 14:52:42 +0800 Subject: [Neuroimaging] Append two nifti images Message-ID: Dear Sir, I want to append two nifti format images. How can i do this..Please let me know. I have attached files along with this mail.. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pred1.nii.gz Type: application/x-gzip Size: 151536 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: subject_9_label.nii.gz Type: application/x-gzip Size: 129525 bytes Desc: not available URL: From arokem at gmail.com Tue Nov 28 09:23:52 2017 From: arokem at gmail.com (Ariel Rokem) Date: Tue, 28 Nov 2017 06:23:52 -0800 Subject: [Neuroimaging] Append two nifti images In-Reply-To: References: Message-ID: Hi Saqib, You might want to look into using nibabel for this: Here's a guide on getting started: http://nipy.org/nibabel/gettingstarted.html Cheers, Ariel On Sun, Nov 26, 2017 at 10:52 PM, Saqib Qamar wrote: > Dear Sir, > I want to append two nifti format images. How can i do this..Please let me > know. I have attached files along with this mail.. > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From effigies at bu.edu Tue Nov 28 10:08:32 2017 From: effigies at bu.edu (Christopher Markiewicz) Date: Tue, 28 Nov 2017 10:08:32 -0500 Subject: [Neuroimaging] Append two nifti images In-Reply-To: References: Message-ID: Hi, These images don't share orientation information, and even assuming that the orientation affine from subject_9_label.nii.gz should be applied to pred1.nii.gz, they are not aligned. They are either flipped posterior/anterior or rotated around the inferior/superior axis. (I suspect the former.) It is difficult to give advice from this starting point, as, if it is straightforwardly applied, you are very likely to get incoherent results. You may want to check your pipeline to ensure that orientation information is being preserved at each step. Once you have aligned images, further operations can begin to make sense. Finally, I assume that by "append", you mean to concatenate the images such that you get a 4D image with 2 time points. For this you can use nibabel (see, e.g., nibabel.concat_images), as Ariel suggests, or standard command-line tools like mri_concat (FreeSurfer) or fslmerge (FSL). Chris On Mon, Nov 27, 2017 at 1:52 AM, Saqib Qamar wrote: > Dear Sir, > I want to append two nifti format images. How can i do this..Please let me > know. I have attached files along with this mail.. > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: