From garyfallidis at gmail.com Mon Aug 6 12:13:45 2018 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Mon, 6 Aug 2018 12:13:45 -0400 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development Message-ID: Dear all, We are happy to announce that the DIPY project has received a three-year R01 grant from the National Institutes of Health under the CRCNS (Collaborative Research in Computational Neuroscience) program. The grant, entitled: ?Community-supported open-source software for computational neuroanatomy? is a collaboration between myself (Indiana University) and Ariel Rokem (University of Washington). It will support the continued development of DIPY, through partial support for the salary of a software engineer, and sharing of new algorithms and data through DIPY, as well as the development of APIs for cloud deployment of DIPY computations. We would like to thank everyone who provided letters of collaboration for our application. The support that we have received from the community has been truly inspiring. Finally, this R01 will be partially funding an annual DIPY workshop which will take place at Indiana University. Dates for the first event will be announced shortly. Best regards, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 +1 (812) 856-5240 https://grg.sice.indiana.edu http://dipy.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From kw401 at cam.ac.uk Mon Aug 6 12:27:58 2018 From: kw401 at cam.ac.uk (Kirstie Whitaker) Date: Mon, 6 Aug 2018 09:27:58 -0700 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congratulations DIPY team!! Really great news :) Kx On Mon, 6 Aug 2018 at 09:14, Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > 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 matthew.brett at gmail.com Mon Aug 6 12:34:21 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Mon, 6 Aug 2018 17:34:21 +0100 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: On Mon, Aug 6, 2018 at 5:13 PM, Eleftherios Garyfallidis wrote: > Dear all, > > We are happy to announce that the DIPY project has received a three-year R01 > grant from the National Institutes of Health under the CRCNS (Collaborative > Research in Computational Neuroscience) program. The grant, entitled: > ?Community-supported open-source software for computational neuroanatomy? is > a collaboration between myself (Indiana University) and Ariel Rokem > (University of Washington). It will support the continued development of > DIPY, through partial support for the salary of a software engineer, and > sharing of new algorithms and data through DIPY, as well as the development > of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. Great work - very well done ... Matthew From ghoshbishakh at gmail.com Mon Aug 6 12:42:07 2018 From: ghoshbishakh at gmail.com (Bishakh Ghosh) Date: Mon, 6 Aug 2018 22:12:07 +0530 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congratulations!! :) On Mon, Aug 6, 2018 at 9:58 PM Kirstie Whitaker wrote: > Congratulations DIPY team!! Really great news :) > > Kx > > On Mon, 6 Aug 2018 at 09:14, Eleftherios Garyfallidis < > garyfallidis at gmail.com> wrote: > >> Dear all, >> >> We are happy to announce that the DIPY project has received a three-year >> R01 grant from the National Institutes of Health under the CRCNS >> (Collaborative Research in Computational Neuroscience) program. The grant, >> entitled: ?Community-supported open-source software for computational >> neuroanatomy? is a collaboration between myself (Indiana University) and >> Ariel Rokem (University of Washington). It will support the continued >> development of DIPY, through partial support for the salary of a software >> engineer, and sharing of new algorithms and data through DIPY, as well as >> the development of APIs for cloud deployment of DIPY computations. >> >> We would like to thank everyone who provided letters of collaboration for >> our application. The support that we have received from the community has >> been truly inspiring. >> >> Finally, this R01 will be partially funding an annual DIPY workshop which >> will take place at Indiana University. Dates for the first event will be >> announced shortly. >> >> Best regards, >> Eleftherios Garyfallidis, PhD >> Assistant Professor >> Intelligent Systems Engineering >> Indiana University >> Luddy Hall 700 N Woodlawn >> Bloomington, IN 47408 >> +1 (812) 856-5240 >> https://grg.sice.indiana.edu >> http://dipy.org >> _______________________________________________ >> 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 > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Mon Aug 6 12:44:51 2018 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Mon, 6 Aug 2018 18:44:51 +0200 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Great news. Well done ! JON HAITZ -- On 6 August 2018 at 18:34, Matthew Brett wrote: > On Mon, Aug 6, 2018 at 5:13 PM, Eleftherios Garyfallidis > wrote: >> Dear all, >> >> We are happy to announce that the DIPY project has received a three-year R01 >> grant from the National Institutes of Health under the CRCNS (Collaborative >> Research in Computational Neuroscience) program. The grant, entitled: >> ?Community-supported open-source software for computational neuroanatomy? is >> a collaboration between myself (Indiana University) and Ariel Rokem >> (University of Washington). It will support the continued development of >> DIPY, through partial support for the salary of a software engineer, and >> sharing of new algorithms and data through DIPY, as well as the development >> of APIs for cloud deployment of DIPY computations. >> >> We would like to thank everyone who provided letters of collaboration for >> our application. The support that we have received from the community has >> been truly inspiring. >> >> Finally, this R01 will be partially funding an annual DIPY workshop which >> will take place at Indiana University. Dates for the first event will be >> announced shortly. > > Great work - very well done ... > > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging From Reid.Robert at mayo.edu Mon Aug 6 12:17:22 2018 From: Reid.Robert at mayo.edu (Reid, Robert I. (Rob)) Date: Mon, 06 Aug 2018 16:17:22 +0000 Subject: [Neuroimaging] [EXTERNAL] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: This is great news! Rob -- Robert I. Reid, Ph.D., Sr. Analyst/Programmer, Information Technology Aging and Dementia Imaging Research, Mayo Clinic 200 First Street SW, Rochester, MN 55905, mayoclinic.org From: Neuroimaging [mailto:neuroimaging-bounces+reid.robert=mayo.edu at python.org] On Behalf Of Eleftherios Garyfallidis Sent: Monday, August 06, 2018 11:14 AM To: Neuroimaging analysis in Python Subject: [EXTERNAL] [Neuroimaging] DIPY researchers receive NIH grant to support development Dear all, We are happy to announce that the DIPY project has received a three-year R01 grant from the National Institutes of Health under the CRCNS (Collaborative Research in Computational Neuroscience) program. The grant, entitled: ?Community-supported open-source software for computational neuroanatomy? is a collaboration between myself (Indiana University) and Ariel Rokem (University of Washington). It will support the continued development of DIPY, through partial support for the salary of a software engineer, and sharing of new algorithms and data through DIPY, as well as the development of APIs for cloud deployment of DIPY computations. We would like to thank everyone who provided letters of collaboration for our application. The support that we have received from the community has been truly inspiring. Finally, this R01 will be partially funding an annual DIPY workshop which will take place at Indiana University. Dates for the first event will be announced shortly. Best regards, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 +1 (812) 856-5240 https://grg.sice.indiana.edu http://dipy.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From satra at mit.edu Mon Aug 6 13:13:12 2018 From: satra at mit.edu (Satrajit Ghosh) Date: Mon, 6 Aug 2018 10:13:12 -0700 Subject: [Neuroimaging] [EXTERNAL] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: congratulations eleftherios and ariel! wonderful news. cheers, satra On Mon, Aug 6, 2018 at 9:51 AM Reid, Robert I. (Rob) via Neuroimaging < neuroimaging at python.org> wrote: > This is great news! > > > > Rob > > > > -- > > Robert I. Reid, Ph.D., Sr. Analyst/Programmer, Information Technology > > Aging and Dementia Imaging Research, Mayo Clinic > > 200 First Street SW, Rochester, MN 55905, mayoclinic.org > > > > > *From:* Neuroimaging [mailto:neuroimaging-bounces+reid.robert= > mayo.edu at python.org] *On Behalf Of *Eleftherios Garyfallidis > *Sent:* Monday, August 06, 2018 11:14 AM > *To:* Neuroimaging analysis in Python > *Subject:* [EXTERNAL] [Neuroimaging] DIPY researchers receive NIH grant > to support development > > > > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dan.lurie at berkeley.edu Mon Aug 6 13:24:21 2018 From: dan.lurie at berkeley.edu (Dan Lurie) Date: Mon, 6 Aug 2018 10:24:21 -0700 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: Message-ID: <32717691-f2a8-44b3-ba5a-ea4df9befb8c@Dan-Luries-iPhone> This is wonderful, congratulations! Dan Lurie Graduate Student Department of Psychology University of California, Berkeley http://despolab.berkeley.edu/lurie > > On Aug 6, 2018 at 09:13, wrote: > > > > Dear all, > > We are happy to announce that the DIPY project has received a three-year R01 grant from the National Institutes of Health under the CRCNS (Collaborative Research in Computational Neuroscience) program. The grant, entitled: ?Community-supported open-source software for computational neuroanatomy? is a collaboration between myself (Indiana University) and Ariel Rokem (University of Washington). It will support the continued development of DIPY, through partial support for the salary of a software engineer, and sharing of new algorithms and data through DIPY, as well as the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for our application. The support that we have received from the community has been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which will take place at Indiana University. Dates for the first event will be announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu (https://grg.sice.indiana.edu/) > http://dipy.org (http://dipy.org/) _______________________________________________ Neuroimaging mailing list Neuroimaging at python.org https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From jevillalonr at gmail.com Mon Aug 6 15:40:42 2018 From: jevillalonr at gmail.com (=?UTF-8?Q?Julio_Villal=C3=B3n?=) Date: Mon, 6 Aug 2018 12:40:42 -0700 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congrats Eleftherios and Ariel!!! El lun., 6 ago. 2018 a las 9:14, Eleftherios Garyfallidis (< garyfallidis at gmail.com>) escribi?: > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Mon Aug 6 15:53:06 2018 From: bertrand.thirion at inria.fr (bthirion) Date: Mon, 6 Aug 2018 21:53:06 +0200 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congratulations ! B >> Dear all, >> >> We are happy to announce that the DIPY project has received a three-year R01 >> grant from the National Institutes of Health under the CRCNS (Collaborative >> Research in Computational Neuroscience) program. The grant, entitled: >> ?Community-supported open-source software for computational neuroanatomy? is >> a collaboration between myself (Indiana University) and Ariel Rokem >> (University of Washington). It will support the continued development of >> DIPY, through partial support for the salary of a software engineer, and >> sharing of new algorithms and data through DIPY, as well as the development >> of APIs for cloud deployment of DIPY computations. >> >> We would like to thank everyone who provided letters of collaboration for >> our application. The support that we have received from the community has >> been truly inspiring. >> >> Finally, this R01 will be partially funding an annual DIPY workshop which >> will take place at Indiana University. Dates for the first event will be >> announced shortly. From yoh at onerussian.com Mon Aug 6 18:45:44 2018 From: yoh at onerussian.com (Yaroslav Halchenko) Date: Mon, 06 Aug 2018 18:45:44 -0400 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Woohoo, congrats! So should now DiPy booth supersede they NeuroDebian one at SfN? :-) On August 6, 2018 12:13:45 PM EDT, Eleftherios Garyfallidis wrote: >Dear all, > >We are happy to announce that the DIPY project has received a >three-year >R01 grant from the National Institutes of Health under the CRCNS >(Collaborative Research in Computational Neuroscience) program. The >grant, >entitled: ?Community-supported open-source software for computational >neuroanatomy? is a collaboration between myself (Indiana University) >and >Ariel Rokem (University of Washington). It will support the continued >development of DIPY, through partial support for the salary of a >software >engineer, and sharing of new algorithms and data through DIPY, as well >as >the development of APIs for cloud deployment of DIPY computations. > >We would like to thank everyone who provided letters of collaboration >for >our application. The support that we have received from the community >has >been truly inspiring. > >Finally, this R01 will be partially funding an annual DIPY workshop >which >will take place at Indiana University. Dates for the first event will >be >announced shortly. > >Best regards, >Eleftherios Garyfallidis, PhD >Assistant Professor >Intelligent Systems Engineering >Indiana University >Luddy Hall 700 N Woodlawn >Bloomington, IN 47408 >+1 (812) 856-5240 >https://grg.sice.indiana.edu >http://dipy.org -- Sent from a phone which beats iPhone. -------------- next part -------------- An HTML attachment was scrubbed... URL: From demian.wassermann at inria.fr Tue Aug 7 02:12:09 2018 From: demian.wassermann at inria.fr (Demian Wassermann) Date: Tue, 7 Aug 2018 08:12:09 +0200 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congrats! -- Demian Wassermann, PhD demian.wassermann at inria.fr Associate Research Professor (CRN) Parietal Team INRIA Saclay Ile-de-France 1 Rue Honor? d'Estienne d'Orves, 91120 Palaiseau > On 6 Aug 2018, at 18:13, Eleftherios Garyfallidis wrote: > > Dear all, > > We are happy to announce that the DIPY project has received a three-year R01 grant from the National Institutes of Health under the CRCNS (Collaborative Research in Computational Neuroscience) program. The grant, entitled: ?Community-supported open-source software for computational neuroanatomy? is a collaboration between myself (Indiana University) and Ariel Rokem (University of Washington). It will support the continued development of DIPY, through partial support for the salary of a software engineer, and sharing of new algorithms and data through DIPY, as well as the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for our application. The support that we have received from the community has been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which will take place at Indiana University. Dates for the first event will be announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging From j.schreiber at fz-juelich.de Tue Aug 7 03:40:01 2018 From: j.schreiber at fz-juelich.de (Jan Schreiber) Date: Tue, 7 Aug 2018 09:40:01 +0200 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: <2f2345a1-d861-c637-aec7-a11e69e18fa6@fz-juelich.de> That's great! Congratulations and thanks for your efforts and this fantastic software library! :-) Cheers, Jan On 08/06/2018 06:13 PM, Eleftherios Garyfallidis wrote: > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The > grant, entitled: ?Community-supported open-source software for > computational neuroanatomy? is a collaboration between myself (Indiana > University) and Ariel Rokem (University of Washington). It will support > the continued development of DIPY, through partial support for the > salary of a software engineer, and sharing of new algorithms and data > through DIPY, as well as the development of APIs for cloud deployment of > DIPY computations. > > We would like to thank everyone who provided letters of collaboration > for our application. The support that we have received from the > community has been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop > which will take place at Indiana University. Dates for the first event > will be announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 5098 bytes Desc: S/MIME Cryptographic Signature URL: From gael.varoquaux at normalesup.org Tue Aug 7 14:58:31 2018 From: gael.varoquaux at normalesup.org (Gael Varoquaux) Date: Tue, 7 Aug 2018 20:58:31 +0200 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: <201808070854.w778skfN095750@nef2.ens.fr> References: <201808070854.w778skfN095750@nef2.ens.fr> Message-ID: <20180807185831.ybr53yroug3to6al@phare.normalesup.org> This is very cool!!! Ga?l On Mon, Aug 06, 2018 at 12:13:45PM -0400, Eleftherios Garyfallidis wrote: > Dear all, > We are happy to announce that the DIPY project has received a three-year R01 > grant from the National Institutes of Health under the CRCNS (Collaborative > Research in Computational Neuroscience) program. The grant, entitled: > ?Community-supported open-source software for computational neuroanatomy? is a > collaboration between myself (Indiana University) and Ariel Rokem (University > of Washington). It will support the continued development of DIPY, through > partial support for the salary of a software engineer, and sharing of new > algorithms and data through DIPY, as well as the development of APIs for cloud > deployment of DIPY computations. > We would like to thank everyone who provided letters of collaboration for our > application. The support that we have received from the community has been > truly inspiring. > Finally, this R01 will be partially funding an annual DIPY workshop which will > take place at Indiana University. Dates for the first event will be announced > shortly. > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -- Gael Varoquaux Senior Researcher, INRIA Parietal NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France Phone: ++ 33-1-69-08-79-68 http://gael-varoquaux.info http://twitter.com/GaelVaroquaux From alexandra.badea at duke.edu Wed Aug 8 04:50:02 2018 From: alexandra.badea at duke.edu (Alexandra Badea, Ph.D.) Date: Wed, 8 Aug 2018 08:50:02 +0000 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congrats!!! Well deserved! Alex Alexandra Badea, PhD Associate Professor Center for InVivo Microscopy Department of Radiology Duke University Medical Center ________________________________ From: Neuroimaging on behalf of Eleftherios Garyfallidis Sent: Monday, August 6, 2018 12:13:45 PM To: Neuroimaging analysis in Python Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development Dear all, We are happy to announce that the DIPY project has received a three-year R01 grant from the National Institutes of Health under the CRCNS (Collaborative Research in Computational Neuroscience) program. The grant, entitled: ?Community-supported open-source software for computational neuroanatomy? is a collaboration between myself (Indiana University) and Ariel Rokem (University of Washington). It will support the continued development of DIPY, through partial support for the salary of a software engineer, and sharing of new algorithms and data through DIPY, as well as the development of APIs for cloud deployment of DIPY computations. We would like to thank everyone who provided letters of collaboration for our application. The support that we have received from the community has been truly inspiring. Finally, this R01 will be partially funding an annual DIPY workshop which will take place at Indiana University. Dates for the first event will be announced shortly. Best regards, Eleftherios Garyfallidis, PhD Assistant Professor Intelligent Systems Engineering Indiana University Luddy Hall 700 N Woodlawn Bloomington, IN 47408 +1 (812) 856-5240 https://grg.sice.indiana.edu http://dipy.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From elef at indiana.edu Sat Aug 11 21:54:14 2018 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Sat, 11 Aug 2018 21:54:14 -0400 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Thank you all for your supportive comments. Happy to be part of the ecosystem. Yarik, a booth at SfN is a great idea (for next year) and definitely planning to be returning back at OHBM this summer. Best, Eleftherios On Wed, Aug 8, 2018 at 5:17 AM Alexandra Badea, Ph.D. < alexandra.badea at duke.edu> wrote: > Congrats!!! Well deserved! > Alex > > Alexandra Badea, PhD > Associate Professor > Center for InVivo Microscopy > Department of Radiology > Duke University Medical Center > ------------------------------ > *From:* Neuroimaging duke.edu at python.org> on behalf of Eleftherios Garyfallidis < > garyfallidis at gmail.com> > *Sent:* Monday, August 6, 2018 12:13:45 PM > > *To:* Neuroimaging analysis in Python > *Subject:* [Neuroimaging] DIPY researchers receive NIH grant to support > development > > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 <+1%20812-856-5240> > https://grg.sice.indiana.edu > > http://dipy.org > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From krzysztof.gorgolewski at gmail.com Sun Aug 12 00:33:50 2018 From: krzysztof.gorgolewski at gmail.com (Chris Gorgolewski) Date: Sun, 12 Aug 2018 00:33:50 -0400 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Congratulations - well deserved! Best, Chris On Mon, Aug 6, 2018, 9:14 AM Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.davidgriffiths at gmail.com Sun Aug 12 09:25:01 2018 From: j.davidgriffiths at gmail.com (John Griffiths) Date: Sun, 12 Aug 2018 09:25:01 -0400 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Nice one dipy team! On Mon, 6 Aug 2018 at 12:14, Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -- Dr. John Griffiths Post-Doctoral Research Fellow Rotman Research Institute, Baycrest Toronto, Canada and Honorary Associate School of Physics University of Sydney -------------- next part -------------- An HTML attachment was scrubbed... URL: From st_gc at hotmail.fr Sun Aug 12 16:21:44 2018 From: st_gc at hotmail.fr (SMAIL Tayeb) Date: Sun, 12 Aug 2018 20:21:44 +0000 Subject: [Neuroimaging] TR: Save file as .img In-Reply-To: References: , Message-ID: Hello I need to know if I can save a matrix (array) as Disc Image File .img My best regards [cid:9cf00a56-a965-4d5a-a835-6578e453746c] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 38462795_1898950803495966_5739267782923517952_n.jpg Type: image/jpeg Size: 6172 bytes Desc: 38462795_1898950803495966_5739267782923517952_n.jpg URL: From markiewicz at stanford.edu Mon Aug 13 09:20:08 2018 From: markiewicz at stanford.edu (Christopher Markiewicz) Date: Mon, 13 Aug 2018 13:20:08 +0000 Subject: [Neuroimaging] Save file as .img In-Reply-To: References: , , Message-ID: Hi Smail, There isn't enough information to answer your question, here. What sort of data is in your matrix, and what do you typically use .img files for? Are there associated .hdr files? If not, you're unlikely to be using neuroimages, and I'm not sure we will be very useful to you on the neuroimaging mailing list. If so, could you give a demonstration of how you're constructing your matrix? For instance, import nibabel as nb img = nib.load('input.img') data_matrix = some_function(img.get_fdata()) Also, this is a pretty broad set of mailing lists that you're cross-posting to. I would suggest you try to limit your posts specifically to the relevant mailing list(s). Best, Chris ________________________________ From: Neuroimaging on behalf of SMAIL Tayeb Sent: Sunday, August 12, 2018 4:21:44 PM To: edu-sig at python.org; db-sig at python.org; datetime-sig at python.org; neuroimaging at python.org; image-sig at python.org; import-sig at python.org; stdlib-sig at python.org; scipy-user at python.org; web-sig at python.org Subject: [Neuroimaging] TR: Save file as .img Hello I need to know if I can save a matrix (array) as Disc Image File .img My best regards [cid:9cf00a56-a965-4d5a-a835-6578e453746c] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 38462795_1898950803495966_5739267782923517952_n.jpg Type: image/jpeg Size: 6172 bytes Desc: 38462795_1898950803495966_5739267782923517952_n.jpg URL: From matthew.brett at gmail.com Mon Aug 13 10:17:18 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Mon, 13 Aug 2018 15:17:18 +0100 Subject: [Neuroimaging] Save file as .img In-Reply-To: References: Message-ID: Hi, On Mon, Aug 13, 2018 at 2:20 PM, Christopher Markiewicz wrote: > > Hi Smail, > > > There isn't enough information to answer your question, here. What sort of data is in your matrix, and what do you typically use .img files for? Are there associated .hdr files? If not, you're unlikely to be using neuroimages, and I'm not sure we will be very useful to you on the neuroimaging mailing list. If so, could you give a demonstration of how you're constructing your matrix? For instance, > > > import nibabel as nb > > img = nib.load('input.img') > > data_matrix = some_function(img.get_fdata()) > > > Also, this is a pretty broad set of mailing lists that you're cross-posting to. I would suggest you try to limit your posts specifically to the relevant mailing list(s). Yes, right. If I had to guess, I would guess that you don't mean a 'disk image file' (which is a Mac installation format), but you might mean something like an Analyze or NIfTI image (neuroimaging formats which also have an .img extension). We really do need more information about what you're trying to do. Cheers, Matthew From iannimmosmith at gmail.com Tue Aug 14 14:54:09 2018 From: iannimmosmith at gmail.com (Ian Nimmo-Smith) Date: Tue, 14 Aug 2018 19:54:09 +0100 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: To Infinity - and beyond!!!! Greetings to the DIPY community. Ian On 6 August 2018 at 17:13, Eleftherios Garyfallidis wrote: > Dear all, > > We are happy to announce that the DIPY project has received a three-year > R01 grant from the National Institutes of Health under the CRCNS > (Collaborative Research in Computational Neuroscience) program. The grant, > entitled: ?Community-supported open-source software for computational > neuroanatomy? is a collaboration between myself (Indiana University) and > Ariel Rokem (University of Washington). It will support the continued > development of DIPY, through partial support for the salary of a software > engineer, and sharing of new algorithms and data through DIPY, as well as > the development of APIs for cloud deployment of DIPY computations. > > We would like to thank everyone who provided letters of collaboration for > our application. The support that we have received from the community has > been truly inspiring. > > Finally, this R01 will be partially funding an annual DIPY workshop which > will take place at Indiana University. Dates for the first event will be > announced shortly. > > Best regards, > Eleftherios Garyfallidis, PhD > Assistant Professor > Intelligent Systems Engineering > Indiana University > Luddy Hall 700 N Woodlawn > Bloomington, IN 47408 > +1 (812) 856-5240 > https://grg.sice.indiana.edu > http://dipy.org > > _______________________________________________ > 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 Tue Aug 14 15:13:15 2018 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Tue, 14 Aug 2018 15:13:15 -0400 Subject: [Neuroimaging] DIPY researchers receive NIH grant to support development In-Reply-To: References: Message-ID: Thank you Ian and John! Inf+!!! :) On Tue, Aug 14, 2018 at 2:54 PM Ian Nimmo-Smith wrote: > To Infinity - and beyond!!!! > > Greetings to the DIPY community. > > Ian > On 6 August 2018 at 17:13, Eleftherios Garyfallidis < > garyfallidis at gmail.com> wrote: > >> Dear all, >> >> We are happy to announce that the DIPY project has received a three-year >> R01 grant from the National Institutes of Health under the CRCNS >> (Collaborative Research in Computational Neuroscience) program. The grant, >> entitled: ?Community-supported open-source software for computational >> neuroanatomy? is a collaboration between myself (Indiana University) and >> Ariel Rokem (University of Washington). It will support the continued >> development of DIPY, through partial support for the salary of a software >> engineer, and sharing of new algorithms and data through DIPY, as well as >> the development of APIs for cloud deployment of DIPY computations. >> >> We would like to thank everyone who provided letters of collaboration for >> our application. The support that we have received from the community has >> been truly inspiring. >> >> Finally, this R01 will be partially funding an annual DIPY workshop which >> will take place at Indiana University. Dates for the first event will be >> announced shortly. >> >> Best regards, >> Eleftherios Garyfallidis, PhD >> Assistant Professor >> Intelligent Systems Engineering >> Indiana University >> Luddy Hall 700 N Woodlawn >> Bloomington, IN 47408 >> +1 (812) 856-5240 <+1%20812-856-5240> >> https://grg.sice.indiana.edu >> http://dipy.org >> >> _______________________________________________ >> 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 matthew.brett at gmail.com Wed Aug 22 06:12:42 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 22 Aug 2018 11:12:42 +0100 Subject: [Neuroimaging] Committing to Open Source in Neuroscience: an invitation Message-ID: Hi, I just got this email via the Nitric mailing list - I'm sure lots of us on this mailing list would consider supporting the initiative. Dear Colleagues, Last year several neuroscientists and computer scientists published an Open Letter pledging to make all essential parts of their research output open source. Importantly, the signatories of the letter will require the same level of openness in work they are asked to review. We invite all like-minded scientists, developers, users, and peers to join us in this commitment and encourage everyone to sign the letter at opensourceforneuroscience.org FAQs on this initiative and a link to a recent "NeuroView" commentary published by the journal Neuron on the open letter arealso available at the above link. Best regards, ---------------- Giorgio Ascoli, PhD University Professor Bioengineering Department,Volgenau School of Engineering Neuroscience Program,Krasnow Institute for Advanced Study Director, Center forNeural Informatics, Structures, & Plasticity MS2A1 - George MasonUniversity, Fairfax, VA 22030-4444 Ph.+1(703)993-4383/+1(703)673-8894 Author of "Trees of theBrain, Roots of the Mind" (MIT Press, 2015) Founding Editor-in-Chief,Neuroinformatics From alexandre.gramfort at inria.fr Mon Aug 27 06:52:23 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Mon, 27 Aug 2018 12:52:23 +0200 Subject: [Neuroimaging] [ANN] OpenMEEG 2.4 release Message-ID: Dear community, We are pleased to announce the new 2.4 release of OpenMEEG. Last release from OpenMEEG was a while ago but a number of developments and bug fixes have been done since then and just needed to be released. A few highlights ============ - Support for non-nested geometries (e.g. hole in skull) - Python bindings work now for both Python 2 and 3 in Windows, Linux and OSX platforms. - Openmeeg can now be installed though conda. See installation for details, this installs the OpenMEEG libraries, binaries and bindings. - Project was moved to GitHub: https://github.com/openmeeg/openmeeg and continuous integration is now done with Travis and Appveyor that also generate nightly builds for all 3 platforms. - Improved web site at https://openmeeg.github.io/ - New tutorial page at : https://openmeeg.github.io/tutorial.html - Optimized parallel computation of the D operator (should accelerate Head matrix computation with OpenMP parallel binaries) - All files saved and written by OpenMEEG are now in Matlab 7.3 / HDF5 format so can be accessed just with load and save in Matlab. Thanks ====== Many thanks to Fran?ois Tadel to help us with the Brainstorm integration and to Sarang Dalal for revamping the Fieldtrip code to better support this new version. Warning ====== If you have used OpenMEEG before you will need to recompute all the intermediate files to use them with the version 2.4 Installation ======== The latest release precompiled binaries are available at: http://openmeeg.gforge.inria.fr/download/?C=M;O=D The precompiled Python extension can now be installed with Anaconda python distribution: conda install -c conda-forge openmeeg. Should you have any issue with this release please report it on the issue tracker on github: https://github.com/openmeeg/openmeeg/issues Regards, The OpenMEEG developers People who contributed to OpenMEEG (in alphabetical order) since the beginning: Alexandre Gramfort Boris Burle Daniel Miklody Emmanuel Olivi Joan Massich Kai Dang Kyle Beauchamp Marmaduke Woodman Maureen Clerc Perrine Landreau Renaud Keriven Sylvain Vallaghe Theodore Papadopoulo Thierry Guillemot Yaroslav Halchenko From pinghongyeh at gmail.com Thu Aug 30 14:43:50 2018 From: pinghongyeh at gmail.com (Ping-Hong Yeh) Date: Thu, 30 Aug 2018 14:43:50 -0400 Subject: [Neuroimaging] [DIPY] DKI free water elimination Message-ID: Hi DIPY users, I would like to know whether there is a FW-DKI module in DIPY. I came across Rafael's free water DKI, https://github.com/RafaelNH/free-water-DKI/blob/master/fwDKI.py Is this compatible with the current DIPY package? Any comments in using this module? Thank you. Ping -------------- next part -------------- An HTML attachment was scrubbed... URL: From rafaelnh21 at gmail.com Fri Aug 31 06:53:17 2018 From: rafaelnh21 at gmail.com (Rafael Henriques) Date: Fri, 31 Aug 2018 11:53:17 +0100 Subject: [Neuroimaging] [DIPY] Re: DKI free water elimination Message-ID: Hi Ping, The code that you find in my pull request was intended to be integrated in Dipy. However, I decided to stop developing a free water DKI model fitting in Dipy, because I noticed that this dramatically compromises both precision and accuracy of kurtosis estimates. If you are interested in suppressing free water partial volume effect in your kurtosis measures, my alternative suggestion is to use the standard free water DTI Dipy's module to obtain a free water volume fraction map. Then you can use this map to remove the voxels of your kurtosis images that contain mostly free water (let's say f>0.5). This procedure will suppress the major free water partial volume contamination without compromising kurtosis precision and accuracy. More information: [Re] Optimization of a free water elimination two-compartment model for diffusion tensor imaging . Best, Rafael >> Hi DIPY users, >> >> I would like to know whether there is a FW-DKI module in DIPY. >> I came across Rafael's free water DKI, >> >> https://github.com/RafaelNH/free-water-DKI/blob/master/fwDKI.py >> >> Is this compatible with the current DIPY package? Any comments in using this >> module? >> >> Thank you. >> >> Ping -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.hoffmann at uni-jena.de Fri Aug 31 08:51:27 2018 From: stefan.hoffmann at uni-jena.de (Stefan Hoffmann) Date: Fri, 31 Aug 2018 14:51:27 +0200 Subject: [Neuroimaging] Affine transformations Message-ID: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de> Dear all, I'm training Neural Networks for Image Registration of T1/T2 images for my master thesis. I'm using the nibabel transformation functions to: Scale, Rotate, Shift batches of my MRI scans using homogeneous coordinates. Therefore I need to rotate and scale around the center of the cropped parts of the scans, while also shifting them. Is there a smart way doing so? I'd be so grateful for response. Best regards, Stefan From matthew.brett at gmail.com Fri Aug 31 09:15:24 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Fri, 31 Aug 2018 14:15:24 +0100 Subject: [Neuroimaging] Affine transformations In-Reply-To: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de> References: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de> Message-ID: Hi, On Fri, Aug 31, 2018 at 1:51 PM, Stefan Hoffmann wrote: > > Dear all, > > I'm training Neural Networks for Image Registration of T1/T2 images for my > master thesis. I'm using the nibabel transformation functions to: > > Scale, Rotate, Shift > > batches of my MRI scans using homogeneous coordinates. Therefore I need to > rotate and scale around the center of the cropped parts of the scans, while > also shifting them. > > Is there a smart way doing so? I don't know about smart, but the standard way to do something like that is to first do a translation to move your desired rotation point to 0, 0, 0, then apply your rotations, then reverse the translation. Let's say your center point was at voxels (2, 3, 4). Then: T = [[1, 0, 0, -2], [0, 1, 0, -3], [0, 0, 1, -4], [0, 0, 0, 1]] The inverse (numpy.linalg.inv(T)) is: Tinv = [[1, 0, 0, 2], [0, 1, 0, 3], [0, 0, 1, 4], [0, 0, 0, 1]] Let's say you have a rotation affine R (for rotation around this point). Your full affine is then Tinv.dot(Z).dot(R).dot(T) I think you'll find that the center doesn't matter for the zooms because, if Z is a zooming affine, and hence of this form: Z = [[a, 0, 0, 0], [0, b, 0, 0], [0, 0, c, 0], [0, 0, 0, 1]] then Tinv.dot(Z).dot(T) == Z for any translations in T. Is that what you mean? Cheers, Matthew From matthew.brett at gmail.com Fri Aug 31 09:26:42 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Fri, 31 Aug 2018 14:26:42 +0100 Subject: [Neuroimaging] Affine transformations In-Reply-To: References: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de> Message-ID: Hi, On Fri, Aug 31, 2018 at 2:15 PM, Matthew Brett wrote: > Hi, > > On Fri, Aug 31, 2018 at 1:51 PM, Stefan Hoffmann > wrote: >> >> Dear all, >> >> I'm training Neural Networks for Image Registration of T1/T2 images for my >> master thesis. I'm using the nibabel transformation functions to: >> >> Scale, Rotate, Shift >> >> batches of my MRI scans using homogeneous coordinates. Therefore I need to >> rotate and scale around the center of the cropped parts of the scans, while >> also shifting them. >> >> Is there a smart way doing so? > > I don't know about smart, but the standard way to do something like > that is to first do a translation to move your desired rotation point > to 0, 0, 0, then apply your rotations, then reverse the translation. > > Let's say your center point was at voxels (2, 3, 4). Then: > > T = [[1, 0, 0, -2], > [0, 1, 0, -3], > [0, 0, 1, -4], > [0, 0, 0, 1]] > > The inverse (numpy.linalg.inv(T)) is: > > Tinv = [[1, 0, 0, 2], > [0, 1, 0, 3], > [0, 0, 1, 4], > [0, 0, 0, 1]] > > Let's say you have a rotation affine R (for rotation around this point). > > Your full affine is then Tinv.dot(Z).dot(R).dot(T) Sorry, editing cruft, I mean: Your full affine is then Tinv.dot(R).dot(T) Cheers, Matthew From stefan.hoffmann at uni-jena.de Fri Aug 31 09:57:59 2018 From: stefan.hoffmann at uni-jena.de (Stefan Hoffmann) Date: Fri, 31 Aug 2018 15:57:59 +0200 Subject: [Neuroimaging] Affine transformations In-Reply-To: References: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de> Message-ID: <20180831155759.Horde.6Gnl-DSjUfjQkw_WgDcx8iE@webmail.uni-jena.de> Dear Matthew, thanks for the fast response. Given center point at voxels (2, 3, 4) so that: T = [[1, 0, 0, -2], [0, 1, 0, -3], [0, 0, 1, -4], [0, 0, 0, 1]] and calculating Tinv.dot(Z).dot(R).dot(T). Would an extra translation T_extra = [[1, 0, 0, -7], [0, 1, 0, 7], [0, 0, 1, -8], [0, 0, 0, 1]] after the rotation be implemented as Tinv.dot(Z).dot(R).dot(T).dot(T_extra) or can it all be done at once with one T: T= [[1, 0, 0, -9], [0, 1, 0, 4], [0, 0, 1, -12], [0, 0, 0, 1]] Also I'd like to ask how to implement the multiplication it in Python? I know there's scipy affine_transformation on the one hand, and also the affine_tarnsform funtion in nipy, but I'm not sure how to use them. Shall I give them the affine matrix Tinv.dot(Z).dot(R).dot(T).dot(T_extra) or it's inverse? best regards, Stefan Quoting Matthew Brett : > Hi, > > On Fri, Aug 31, 2018 at 2:15 PM, Matthew Brett > wrote: >> Hi, >> >> On Fri, Aug 31, 2018 at 1:51 PM, Stefan Hoffmann >> wrote: >>> >>> Dear all, >>> >>> I'm training Neural Networks for Image Registration of T1/T2 images for my >>> master thesis. I'm using the nibabel transformation functions to: >>> >>> Scale, Rotate, Shift >>> >>> batches of my MRI scans using homogeneous coordinates. Therefore I need to >>> rotate and scale around the center of the cropped parts of the scans, while >>> also shifting them. >>> >>> Is there a smart way doing so? >> >> I don't know about smart, but the standard way to do something like >> that is to first do a translation to move your desired rotation point >> to 0, 0, 0, then apply your rotations, then reverse the translation. >> >> Let's say your center point was at voxels (2, 3, 4). Then: >> >> T = [[1, 0, 0, -2], >> [0, 1, 0, -3], >> [0, 0, 1, -4], >> [0, 0, 0, 1]] >> >> The inverse (numpy.linalg.inv(T)) is: >> >> Tinv = [[1, 0, 0, 2], >> [0, 1, 0, 3], >> [0, 0, 1, 4], >> [0, 0, 0, 1]] >> >> Let's say you have a rotation affine R (for rotation around this point). >> >> Your full affine is then Tinv.dot(Z).dot(R).dot(T) > > Sorry, editing cruft, I mean: > > Your full affine is then Tinv.dot(R).dot(T) > > Cheers, > > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging From matthew.brett at gmail.com Fri Aug 31 10:06:55 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Fri, 31 Aug 2018 15:06:55 +0100 Subject: [Neuroimaging] Affine transformations In-Reply-To: <20180831155759.Horde.6Gnl-DSjUfjQkw_WgDcx8iE@webmail.uni-jena.de> References: <20180831145127.Horde.dEbME051yHvSIMhXHdsPte9@webmail.uni-jena.de> <20180831155759.Horde.6Gnl-DSjUfjQkw_WgDcx8iE@webmail.uni-jena.de> Message-ID: Hi, On Fri, Aug 31, 2018 at 2:57 PM, Stefan Hoffmann wrote: > > Dear Matthew, > > thanks for the fast response. > > Given center point at voxels (2, 3, 4) so that: > > T = [[1, 0, 0, -2], > [0, 1, 0, -3], > [0, 0, 1, -4], > [0, 0, 0, 1]] > > and calculating Tinv.dot(Z).dot(R).dot(T). > > Would an extra translation > > T_extra = [[1, 0, 0, -7], > [0, 1, 0, 7], > [0, 0, 1, -8], > [0, 0, 0, 1]] > > after the rotation be implemented as > > Tinv.dot(Z).dot(R).dot(T).dot(T_extra) > > or can it all be done at once with one T: > > T= [[1, 0, 0, -9], > [0, 1, 0, 4], > [0, 0, 1, -12], > [0, 0, 0, 1]] Did you catch: http://nipy.org/nibabel/coordinate_systems.html ? Probably you did. The transformations read from right to left, so read Tinv.dot(Z).dot(R).dot(T).dot(T_extra) as First apply T_extra Then apply T Then apply R Then apply Tinv So, I think you want: T_extra.dot(Tinv).dot(Z).dot(R).dot(T) > Also I'd like to ask how to implement the multiplication it in Python? > > I know there's scipy affine_transformation on the one hand, and also the > affine_tarnsform funtion in nipy, but I'm not sure how to use them. The usual situation is that you first apply the image affine matrix (voxels to RAS mm) then apply any transforms, then apply the inverted image affine (RASmm to voxels). Have a look at: https://bic-berkeley.github.io/psych-214-fall-2016/resampling_with_ndimage.html Does that help to explain how to use the Scipy functions to make a transformed version of the image? Cheers, Matthew From pinghongyeh at gmail.com Fri Aug 31 14:17:34 2018 From: pinghongyeh at gmail.com (Ping-Hong Yeh) Date: Fri, 31 Aug 2018 14:17:34 -0400 Subject: [Neuroimaging] [DIPY] Re: DKI free water elimination In-Reply-To: References: Message-ID: Hi Rafael, Thank you for the clarification. Best, Ping On Fri, Aug 31, 2018 at 6:53 AM Rafael Henriques wrote: > Hi Ping, > > The code that you find in my pull request was intended to be integrated in > Dipy. However, I decided to stop developing a free water DKI model fitting > in Dipy, because I noticed that this dramatically compromises both > precision and accuracy of kurtosis estimates. > > If you are interested in suppressing free water partial volume effect in > your kurtosis measures, my alternative suggestion is to use the standard > free water DTI Dipy's module to obtain a free water volume fraction map. > Then you can use this map to remove the voxels of your kurtosis images that > contain mostly free water (let's say f>0.5). This procedure will suppress > the major free water partial volume contamination without compromising > kurtosis precision and accuracy. > > More information: [Re] Optimization of a free water elimination > two-compartment model for diffusion tensor imaging > > . > > Best, > > Rafael > > >> Hi DIPY users, > >> > >> I would like to know whether there is a FW-DKI module in DIPY. > >> I came across Rafael's free water DKI, > >> > >> https://github.com/RafaelNH/free-water-DKI/blob/master/fwDKI.py > >> > >> Is this compatible with the current DIPY package? Any comments in using > this >> module? > >> > >> Thank you. > >> > >> Ping > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: