From alessandro.stranieri at gmail.com Sat Dec 1 09:30:40 2018 From: alessandro.stranieri at gmail.com (Alessandro Stranieri) Date: Sat, 1 Dec 2018 16:30:40 +0200 Subject: [Neuroimaging] Understanding atlas usage In-Reply-To: References: Message-ID: Hello On Fri, Nov 30, 2018 at 11:59 PM bthirion wrote: > On 30/11/2018 17:26, Alessandro Stranieri wrote: > > Hi, > > I am working on a small project with the adhd data. My background is > software engineering, but I am very new to nipy and neuroscience in general > so I might get some terminology wrong. > > Currently I am working my way through the correlation/connectome examples. > I have a few doubts but, in order to keep it simple, I will just > post a couple, hoping for help. > > You're probably using Nilearn. Could you post these questions on > Neurostars.org, so that other people can benefit from the answers ? > OK, I will do that! > > 1. The fetch_adhd functions states that a maximum of 40 subjects can be > retrieved. This means that if I want to use more, I need to do all the > processing myself from the files at > https://www.nitrc.org. Is it correct? > > Yes. > > 2. nilearn provides some atlases and I have more or less understood how to > use them. However, on NITRC one can also find 2 functional parcellation > templates, and time series are provided > for those parcellations. I think I managed to create and display > connectomes with those templates but, what if I want to know the label of a > region? Those regions are labelled by numbers. > For example, if I use the aal atlas, I can see 'Precentral_L', > 'Precental_R' and so on. Can I do the same with the cc200 for example? I > fear that, since those parcellation are functional > and not anatomical, there are no real labels associated to the region. But > I would still like to have a data-structure that allows me to query things > like: this region is in V1, or in the > frontal lobe or other. > > The best way to learn about parcellations is to run the corresponding > examples of the library. > > Each atlas comes with different information, so you may not have > functional labels if the atlas comes from a functional parcellation, such > as resting-state for instance. > > Thanks! Alessandro > HTH. > > Bertrand > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rdaviet at wharton.upenn.edu Sat Dec 8 04:37:25 2018 From: rdaviet at wharton.upenn.edu (Daviet, Remi) Date: Sat, 8 Dec 2018 09:37:25 +0000 Subject: [Neuroimaging] [nibabel] gifti.py:760: ResourceWarning: unclosed file Message-ID: Hi everyone, opening a gifti file with nib.load() twice seems to return a warning: gifti.py:760: ResourceWarning: unclosed file However, I do not find in the doc how to "unload" the file, to be able to reopen it at a later point without the warning. Any suggestions? Best --- Remi Daviet -------------- next part -------------- An HTML attachment was scrubbed... URL: From john.samoylovich.pellman at gmail.com Sat Dec 8 18:42:34 2018 From: john.samoylovich.pellman at gmail.com (John Pellman) Date: Sat, 8 Dec 2018 18:42:34 -0500 Subject: [Neuroimaging] Colorized CT Scanner Message-ID: This might not be the most appropriate list for this / could be a bit impertinent, but I came across this tech (a CT scanner that makes use of CERN's Medipix photon detector to colorize CT scans), found it really neat, and thought I'd share. Seems like it could be used to produce high quality structural images in animal studies (the ethics of using CT scans in human studies seems a bit more dubious), with well-segmented tissue. https://www.marsbioimaging.com/mars/ https://www.marsbioimaging.com/mars/wp-content/uploads/2018/07/MARS_Electronic.pdf -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Sun Dec 9 10:02:30 2018 From: jbpoline at gmail.com (JB Poline) Date: Sun, 9 Dec 2018 10:02:30 -0500 Subject: [Neuroimaging] Colorized CT Scanner In-Reply-To: References: Message-ID: They are beautiful ! On Sat, Dec 8, 2018 at 6:45 PM John Pellman < john.samoylovich.pellman at gmail.com> wrote: > This might not be the most appropriate list for this / could be a bit > impertinent, but I came across this tech (a CT scanner that makes use of > CERN's Medipix photon detector to colorize CT scans), found it really neat, > and thought I'd share. Seems like it could be used to produce high quality > structural images in animal studies (the ethics of using CT scans in human > studies seems a bit more dubious), with well-segmented tissue. > > https://www.marsbioimaging.com/mars/ > > > https://www.marsbioimaging.com/mars/wp-content/uploads/2018/07/MARS_Electronic.pdf > _______________________________________________ > 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 Sun Dec 9 10:56:41 2018 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Sun, 9 Dec 2018 10:56:41 -0500 Subject: [Neuroimaging] Colorized CT Scanner In-Reply-To: References: Message-ID: +1 On Sun, Dec 9, 2018 at 10:02 AM JB Poline wrote: > They are beautiful ! > > On Sat, Dec 8, 2018 at 6:45 PM John Pellman < > john.samoylovich.pellman at gmail.com> wrote: > >> This might not be the most appropriate list for this / could be a bit >> impertinent, but I came across this tech (a CT scanner that makes use of >> CERN's Medipix photon detector to colorize CT scans), found it really neat, >> and thought I'd share. Seems like it could be used to produce high quality >> structural images in animal studies (the ethics of using CT scans in human >> studies seems a bit more dubious), with well-segmented tissue. >> >> https://www.marsbioimaging.com/mars/ >> >> >> https://www.marsbioimaging.com/mars/wp-content/uploads/2018/07/MARS_Electronic.pdf >> _______________________________________________ >> 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 Sun Dec 9 16:29:14 2018 From: morgan.hough at gmail.com (Morgan Hough) Date: Sun, 9 Dec 2018 21:29:14 +0000 Subject: [Neuroimaging] Colorized CT Scanner Message-ID: That is awesome tech. It sounds like what satellite imaging people would call hyperspectral imaging. Very cool. Thanks for sharing. -------------- next part -------------- An HTML attachment was scrubbed... URL: From satra at mit.edu Mon Dec 10 12:24:46 2018 From: satra at mit.edu (Satrajit Ghosh) Date: Mon, 10 Dec 2018 12:24:46 -0500 Subject: [Neuroimaging] Colorized CT Scanner In-Reply-To: References: Message-ID: very neat. will have to read more about the method. thanks for sharing. cheers, satra On Sun, Dec 9, 2018 at 4:29 PM Morgan Hough wrote: > That is awesome tech. It sounds like what satellite imaging people would > call hyperspectral imaging. Very cool. Thanks for sharing. > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francisco.pereira at gmail.com Mon Dec 10 12:50:57 2018 From: francisco.pereira at gmail.com (Francisco Pereira) Date: Mon, 10 Dec 2018 12:50:57 -0500 Subject: [Neuroimaging] Colorized CT Scanner In-Reply-To: References: Message-ID: There is also this, I think the principle is similar https://www.siemens.com/innovation/en/home/pictures-of-the-future/health-and-well-being/medical-imaging-cinematic-vrt.html cheers, Francisco On Mon, Dec 10, 2018 at 12:30 PM Satrajit Ghosh wrote: > very neat. will have to read more about the method. thanks for sharing. > > cheers, > > satra > > On Sun, Dec 9, 2018 at 4:29 PM Morgan Hough > wrote: > >> That is awesome tech. It sounds like what satellite imaging people would >> call hyperspectral imaging. Very cool. Thanks for sharing. >> _______________________________________________ >> 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 garyfallidis at gmail.com Thu Dec 13 11:38:35 2018 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Thu, 13 Dec 2018 11:38:35 -0500 Subject: [Neuroimaging] ANN: DIPY 0.15.0 release Message-ID: We are excited to announce a new release of Diffusion Imaging in Python (DIPY). DIPY 0.15 (Wednesday, 12 December 2018) This release received contributions from 30 developers (the full release notes are at: http://dipy.org/release0.15.html ) Highlights of this release include: - Updated RecoBundles for automatic anatomical bundle segmentation. - New Reconstruction Model: qtau-dMRI signal representation. - New command line interfaces (e.g., dipy_slr). - New continuous integration with AppVeyor CI. - Nibabel Streamlines API now used almost everywhere for better memory management. - Compatibility with Python 3.7. - Many tutorials added or updated (5 New). - Large overall documentation update. - Moved visualization module to a new library: FURY. - Closed 287 issues and merged 93 pull requests. Want to learn more? The DIPY project is hosting an educational workshop March 11-15 at Indiana University, USA. The event is sponsored by the National Institute of Health (NIH). See topics and detailed information here: https://workshop.dipy.org The workshop will include tutorials on tracking, microstructure, and statistical analysis. The workshop will also include a data accelerator where you will be able to analyze your own data together with the DIPY developers. More than 15 DIPY developers will be available this year on site to help. All tutorials will run on 3 levels: novice, intermediate and advanced. Register here . To upgrade or install DIPY Run the following command in your terminal: pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (2.3.0+). Questions or suggestions? For any questions go to http://dipy.org, or send an e-mail to dipy at python.org We also have an instant messaging service and chat room available at https://gitter.im/nipy/dipy 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 Luca.Cocchi at qimrberghofer.edu.au Mon Dec 17 23:04:31 2018 From: Luca.Cocchi at qimrberghofer.edu.au (Luca Cocchi) Date: Tue, 18 Dec 2018 04:04:31 +0000 Subject: [Neuroimaging] nilearn.image.clean_img Message-ID: <9AA7B3B924D8FF4EA78FC39EE07D1192619CF5D7@EXCH05S.adqimr.ad.lan> Hello, I have a question regarding the "nilearn.image.clean_img" function. The output of this function suggests that the mean signal of each voxel has been removed, even when the options "detrending" and "standardize" are disabled. Is this an expected behaviour? Is it possible to avoid removing the mean signal or, alternatively, put it back after the "cleaning" has been performed? Thank you. Best, Luca -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.muench at research.fchampalimaud.org Wed Dec 19 08:00:37 2018 From: daniel.muench at research.fchampalimaud.org (=?UTF-8?Q?Daniel_M=c3=bcnch?=) Date: Wed, 19 Dec 2018 13:00:37 +0000 Subject: [Neuroimaging] [Nibabel] save modified nifti header to file Message-ID: <0805fec7-ca46-ec6e-34ad-044308813918@research.fchampalimaud.org> Hi, I am loading a nifti1 file using nib.load(), then modify some header fields. When I now save using nib.save() the whole image gets loaded to the memory and saved again (which takes forever). As I only modified the header is there a way to only write these modifications to the file? Thanks, Daniel -- Dr. Daniel M?nch Behavior and Metabolism Lab Champalimaud Centre for the Unknown Av. Bras?lia s/n (Doca de Pedrou?os) 1400-038 Lisboa, Portugal Mobile: +351 916713862 Mail: daniel.muench at research.fchampalimaud.org Web: http://muench.bio Web: http://ribeirolab.org PGP: http://j.mp/PublicKey-Daniel ? From matthew.brett at gmail.com Wed Dec 19 09:12:13 2018 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 19 Dec 2018 14:12:13 +0000 Subject: [Neuroimaging] [Nibabel] save modified nifti header to file In-Reply-To: <0805fec7-ca46-ec6e-34ad-044308813918@research.fchampalimaud.org> References: <0805fec7-ca46-ec6e-34ad-044308813918@research.fchampalimaud.org> Message-ID: Hi, On Wed, Dec 19, 2018 at 1:01 PM Daniel M?nch wrote: > > Hi, > > I am loading a nifti1 file using nib.load(), then modify some header > fields. When I now save using nib.save() the whole image gets loaded to > the memory and saved again (which takes forever). > > As I only modified the header is there a way to only write these > modifications to the file? You could try something like this (assuming the size of the header isn't going to change): [nav] In [18]: with open('test.nii', 'r+b') as fobj: ...: header = nib.Nifti1Header.from_fileobj(fobj) ...: header['descrip'] = b'modified' ...: fobj.seek(0) ...: header.write_to(fobj) Cheers, Matthew From nicole.landi at yale.edu Fri Dec 21 10:04:36 2018 From: nicole.landi at yale.edu (Landi, Nicole) Date: Fri, 21 Dec 2018 15:04:36 +0000 Subject: [Neuroimaging] Postdoctoral Fellowship: Neurobiology of Reading Message-ID: <034786ED-F0E9-4E1D-B65C-B62F0FCE9044@yale.edu> The LandiLab (PI: Nicole Landi https://landi.lab.uconn.edu/) at Haskins Laboratories and the University of Connecticut is seeking to hire a full-time postdoctoral research fellow. Haskins Laboratories https://haskinslabs.org/ is located in New Haven, CT and is closely affiliated with Yale University and the University of Connecticut. This postdoc will join an NIH funded project investigating the neurobiological basis (brain structure, genetics) of reading. The successful applicant will be responsible for conducting and interpreting analyses of neuroimaging data (primarily gray matter structure and diffusion imaging). This position is part of a multi-site project (Haskins Laboratories, Yale University, University of Houston, Baylor College of Medicine, Florida Center for Reading Research) that is analyzing neuroimaging and genotyping data from 9000+ individuals to explore gene-brain-behavior relationships. Required qualifications: ? PhD or equivalent in Psychology, Neuroscience, Cognitive Science, Computer Science, or related field ? Experience analyzing neuroimaging data ? Experience with one or more imaging analysis packages (e.g., FSL, SPM, AFNI, FreeSurfer) ? Programming skills, including knowledge of at least one language and Unix commands ? Proficiency with writing academic manuscripts ? Leadership, communication, and organizational skills Preferred qualifications: ? Experience analyzing diffusion weighted imaging data ? Experience with advanced neuroimaging analysis techniques, e.g., independent components analysis, functional and context-dependent connectivity, VBM, machine learning ? Demonstrable interest in the neurobiology of language and/or reading ? Familiarity with genetic analyses or imaging genetic analyses This postdoctoral scholar will work with an interdisciplinary and highly collaborative team of PIs and affiliated scientists from the LandiLab (PI: Nicole Landi, University of Connecticut, Haskins Laboratories, Yale Child Study Center) and the GENESIS lab (PI: Elena Grigorenko, University of Houston & Baylor College of Medicine, Houston TX).This position is based at Haskins Laboratories (New Haven, CT), but will coordinate with research partners at multiple locations. Interested candidates should send 1) a CV; 2) the names and contact information of three references; and, 3) a cover letter to Dr. Nicole Landi at Nicole.Landi at UConn.edu . This position will remain open until filled; desired start date is Spring 2019. Salary will be commensurate with NIH postdoctoral funding levels. Haskins Laboratories is an equal opportunity employer. -------------- next part -------------- An HTML attachment was scrubbed... URL: From garyfallidis at gmail.com Sat Dec 22 11:28:38 2018 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Sat, 22 Dec 2018 11:28:38 -0500 Subject: [Neuroimaging] ANN: DIPY 0.15.0 release Message-ID: Hello all, We are excited to announce a new release of Diffusion Imaging in Python (DIPY). DIPY 0.15 (Wednesday, 12 December 2018) This release received contributions from 30 developers (the full release notes are at: http://dipy.org/release0.15.html ) Highlights of this release include: - Updated RecoBundles for automatic anatomical bundle segmentation. - New Reconstruction Model: qtau-dMRI signal representation. - New command line interfaces (e.g., dipy_slr). - New continuous integration with AppVeyor CI. - Nibabel Streamlines API now used almost everywhere for better memory management. - Compatibility with Python 3.7. - Many tutorials added or updated (5 New). - Large overall documentation update. - Moved visualization module to a new library: FURY. - Closed 287 issues and merged 93 pull requests. Want to learn more? The DIPY project is hosting an educational workshop March 11-15 at Indiana University, USA. The event is sponsored by the National Institute of Health (NIH). See topics and detailed information here: https://workshop.dipy.org The workshop will include tutorials on tracking, microstructure, and statistical analysis. The workshop will also include a data accelerator where you will be able to analyze your own data together with the DIPY developers. More than 15 DIPY developers will be available this year on site to help. All tutorials will run on 3 levels: novice, intermediate and advanced. Register here . To upgrade or install DIPY Run the following command in your terminal: pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (2.3.0+). Questions or suggestions? For any questions go to http://dipy.org, or send an e-mail to dipy at python.org We also have an instant messaging service and chat room available at https://gitter.im/nipy/dipy 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 satra at mit.edu Sat Dec 22 14:24:17 2018 From: satra at mit.edu (Satrajit Ghosh) Date: Sat, 22 Dec 2018 23:24:17 +0400 Subject: [Neuroimaging] ANN: DIPY 0.15.0 release In-Reply-To: References: Message-ID: congratulations dipy team! cheers, satra On Sat, Dec 22, 2018 at 8:29 PM Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > Hello all, > > We are excited to announce a new release of Diffusion Imaging in Python > (DIPY). > > DIPY 0.15 (Wednesday, 12 December 2018) > > This release received contributions from 30 developers (the full release > notes are at: http://dipy.org/release0.15.html > ) > > Highlights of this release include: > > > - > > Updated RecoBundles for automatic anatomical bundle segmentation. > - > > New Reconstruction Model: qtau-dMRI signal representation. > - > > New command line interfaces (e.g., dipy_slr). > - > > New continuous integration with AppVeyor CI. > - > > Nibabel Streamlines API now used almost everywhere for better memory > management. > - > > Compatibility with Python 3.7. > - > > Many tutorials added or updated (5 New). > - > > Large overall documentation update. > - > > Moved visualization module to a new library: FURY. > - > > Closed 287 issues and merged 93 pull requests. > > > Want to learn more? > > The DIPY project is hosting an educational workshop March 11-15 at Indiana > University, USA. The event is sponsored by the National Institute of Health > (NIH). See topics and detailed information here: > > https://workshop.dipy.org > > The workshop will include tutorials on tracking, microstructure, and > statistical analysis. The workshop will also include a data accelerator > where you will be able to analyze your own data together with the DIPY > developers. More than 15 DIPY developers will be > available this year on site to help. All tutorials will run on 3 levels: > novice, intermediate and advanced. Register here > . > > > To upgrade or install DIPY > > Run the following command in your terminal: > > > pip install --upgrade dipy > > or > > conda install -c conda-forge dipy > > This version of DIPY depends on nibabel (2.3.0+). > > Questions or suggestions? > > For any questions go to http://dipy.org, or send an e-mail to > dipy at python.org > > We also have an instant messaging service and chat room available at > https://gitter.im/nipy/dipy > > On behalf of the DIPY developers, > > Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro > > http://dipy.org/developers.html > > _______________________________________________ > 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 Sat Dec 22 16:18:25 2018 From: elef at indiana.edu (Eleftherios Garyfallidis) Date: Sat, 22 Dec 2018 16:18:25 -0500 Subject: [Neuroimaging] ANN: DIPY 0.15.0 release In-Reply-To: References: Message-ID: Thank you Satra and Happy Holidays to you and all Neuroimagers! On Sat, Dec 22, 2018 at 2:29 PM Satrajit Ghosh wrote: > congratulations dipy team! > > cheers, > > satra > > On Sat, Dec 22, 2018 at 8:29 PM Eleftherios Garyfallidis < > garyfallidis at gmail.com> wrote: > >> Hello all, >> >> We are excited to announce a new release of Diffusion Imaging in Python >> (DIPY). >> >> DIPY 0.15 (Wednesday, 12 December 2018) >> >> This release received contributions from 30 developers (the full release >> notes are at: http://dipy.org/release0.15.html >> ) >> >> Highlights of this release include: >> >> >> - >> >> Updated RecoBundles for automatic anatomical bundle segmentation. >> - >> >> New Reconstruction Model: qtau-dMRI signal representation. >> - >> >> New command line interfaces (e.g., dipy_slr). >> - >> >> New continuous integration with AppVeyor CI. >> - >> >> Nibabel Streamlines API now used almost everywhere for better memory >> management. >> - >> >> Compatibility with Python 3.7. >> - >> >> Many tutorials added or updated (5 New). >> - >> >> Large overall documentation update. >> - >> >> Moved visualization module to a new library: FURY. >> - >> >> Closed 287 issues and merged 93 pull requests. >> >> >> Want to learn more? >> >> The DIPY project is hosting an educational workshop March 11-15 at >> Indiana University, USA. The event is sponsored by the National Institute >> of Health (NIH). See topics and detailed information here: >> >> https://workshop.dipy.org >> >> The workshop will include tutorials on tracking, microstructure, and >> statistical analysis. The workshop will also include a data accelerator >> where you will be able to analyze your own data together with the DIPY >> developers. More than 15 DIPY developers will be >> available this year on site to help. All tutorials will run on 3 levels: >> novice, intermediate and advanced. Register here >> . >> >> >> To upgrade or install DIPY >> >> Run the following command in your terminal: >> >> >> pip install --upgrade dipy >> >> or >> >> conda install -c conda-forge dipy >> >> This version of DIPY depends on nibabel (2.3.0+). >> >> Questions or suggestions? >> >> For any questions go to http://dipy.org, or send an e-mail to >> dipy at python.org >> >> We also have an instant messaging service and chat room available at >> https://gitter.im/nipy/dipy >> >> On behalf of the DIPY developers, >> >> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro >> >> http://dipy.org/developers.html >> >> _______________________________________________ >> 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 gael.varoquaux at normalesup.org Sun Dec 23 11:13:31 2018 From: gael.varoquaux at normalesup.org (Gael Varoquaux) Date: Sun, 23 Dec 2018 17:13:31 +0100 Subject: [Neuroimaging] ANN: DIPY 0.15.0 release In-Reply-To: References: Message-ID: <20181223161331.r6htjuufpes6nlzj@phare.normalesup.org> Hurray! Congratulations. It's a pleasure to see that the Python neuroimaging ecosystem is so healthy! Ga?l On Sat, Dec 22, 2018 at 04:18:25PM -0500, Eleftherios Garyfallidis wrote: > Thank you Satra and Happy?Holidays to you and all Neuroimagers!? > On Sat, Dec 22, 2018 at 2:29 PM Satrajit Ghosh wrote: > congratulations dipy team! > cheers, > satra > On Sat, Dec 22, 2018 at 8:29 PM Eleftherios Garyfallidis < > garyfallidis at gmail.com> wrote: > Hello all, > We are excited to announce a new release of Diffusion Imaging in Python > (DIPY). > DIPY 0.15 (Wednesday, 12 December 2018) > This release received contributions from 30 developers (the full > release notes are at: http://dipy.org/release0.15.html) > Highlights of this release include: > ? Updated RecoBundles for automatic anatomical bundle segmentation. > ? New Reconstruction Model: qtau-dMRI signal representation. > ? New command line interfaces (e.g., dipy_slr). > ? New continuous integration with AppVeyor CI. > ? Nibabel Streamlines API now used almost everywhere for better > memory management. > ? Compatibility with Python 3.7. > ? Many tutorials added or updated (5 New). > ? Large overall documentation update. > ? Moved visualization module to a new library: FURY. > ? Closed 287 issues and merged 93 pull requests. > Want to learn more? > The DIPY project is hosting an educational workshop March 11-15 at > Indiana University, USA. The event is sponsored by the National > Institute of Health (NIH). See topics and detailed information here: > https://workshop.dipy.org > The workshop will include tutorials on tracking, microstructure, and > statistical analysis. The workshop will also include a data accelerator > where you will be able to analyze your own data together with the DIPY > developers. More than 15 DIPY developers will be available this year on > site to help. All tutorials will run on 3 levels: novice, intermediate > and advanced. Register here. > To upgrade or install DIPY > Run the following command in your terminal: > pip install --upgrade dipy > or > conda install -c conda-forge dipy > This version of DIPY depends on nibabel (2.3.0+). > Questions or suggestions? > For any questions go to http://dipy.org, or send an e-mail to > dipy at python.org ? > We also have an instant messaging service and chat room available at > https://gitter.im/nipy/dipy > On behalf of the DIPY developers, > Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro > http://dipy.org/developers.html > _______________________________________________ > 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 -- 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 pinghongyeh at gmail.com Thu Dec 27 09:54:47 2018 From: pinghongyeh at gmail.com (Ping-Hong Yeh) Date: Thu, 27 Dec 2018 09:54:47 -0500 Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI Message-ID: Hi Dipy Users, I've ran into errors "Eigenvalues did not converge" when using the free water elimination model, and here is the error message: File "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py", line 1615, in _decompose_tensor_nan min_diffusivity=min_diffusivity) File "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py", line 1946, in decompose_tensor eigenvals, eigenvecs = eigh(tensor) File "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py", line 128, in eigh return np.linalg.eigh(a, UPLO) File "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 1291, in eigh w, vt = gufunc(a, signature=signature, extobj=extobj) File "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 95, in _raise_linalgerror_eigenvalues_nonconvergence raise LinAlgError("Eigenvalues did not converge") numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge Any suggestions? Thank you. Ping -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Sat Dec 29 01:11:44 2018 From: arokem at gmail.com (Ariel Rokem) Date: Fri, 28 Dec 2018 22:11:44 -0800 Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI In-Reply-To: References: Message-ID: Hi Ping, Thanks for your email. Hard to say exactly what is going on without further information. Could you tell us more about the data you are using? How many b-values? How many directions? Any chance you could share the data from the voxel that caused that error to be raised? Thanks! Ariel On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh wrote: > Hi Dipy Users, > > I've ran into errors "Eigenvalues did not converge" when using the free > water elimination model, > and here is the error message: > > File > "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py", > line 1615, in _decompose_tensor_nan > min_diffusivity=min_diffusivity) > File > "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py", > line 1946, in decompose_tensor > eigenvals, eigenvecs = eigh(tensor) > File > "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py", > line 128, in eigh > return np.linalg.eigh(a, UPLO) > File > "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py", > line 1291, in eigh > w, vt = gufunc(a, signature=signature, extobj=extobj) > File > "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py", > line 95, in _raise_linalgerror_eigenvalues_nonconvergence > raise LinAlgError("Eigenvalues did not converge") > numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge > > > Any suggestions? > > 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: From pinghongyeh at gmail.com Sat Dec 29 18:43:38 2018 From: pinghongyeh at gmail.com (Ping-Hong Yeh) Date: Sat, 29 Dec 2018 18:43:38 -0500 Subject: [Neuroimaging] Fwd: NCNC3344 multi shell DWI In-Reply-To: References: Message-ID: Re: failure using DIPY Free Water Elimination DTI Hi Ariel, Please find the link for the multishell DWI (90 directions for each shell with b=3000,2000,1000 plus 19 b0) data. There is no error using the same data for other models. e.g. NLLS DKI, and CSD, sfm for fiber tracking. Thank you. Ping Hi Ping, Thanks for your email. Hard to say exactly what is going on without further information. Could you tell us more about the data you are using? How many b-values? How many directions? Any chance you could share the data from the voxel that caused that error to be raised? Thanks! Ariel multishelldwi.tar -------------- next part -------------- An HTML attachment was scrubbed... URL: From pinghongyeh at gmail.com Mon Dec 31 08:43:14 2018 From: pinghongyeh at gmail.com (Ping-Hong Yeh) Date: Mon, 31 Dec 2018 08:43:14 -0500 Subject: [Neuroimaging] failure using DIPY Free Water Elimination DTI In-Reply-To: References: Message-ID: Hi Ariel, Have you got the chance to look at the DWI data that was attached to the previous email? Thank you for your time. Ping On Sat, Dec 29, 2018 at 1:12 AM Ariel Rokem wrote: > Hi Ping, > > Thanks for your email. Hard to say exactly what is going on without > further information. Could you tell us more about the data you are using? > How many b-values? How many directions? Any chance you could share the data > from the voxel that caused that error to be raised? > > Thanks! > > Ariel > > On Thu, Dec 27, 2018 at 6:55 AM Ping-Hong Yeh > wrote: > >> Hi Dipy Users, >> >> I've ran into errors "Eigenvalues did not converge" when using the free >> water elimination model, >> and here is the error message: >> >> File >> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py", >> line 1615, in _decompose_tensor_nan >> min_diffusivity=min_diffusivity) >> File >> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/reconst/dti.py", >> line 1946, in decompose_tensor >> eigenvals, eigenvecs = eigh(tensor) >> File >> "/Users/yehp/anaconda3/lib/python3.6/site-packages/dipy/utils/arrfuncs.py", >> line 128, in eigh >> return np.linalg.eigh(a, UPLO) >> File >> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py", >> line 1291, in eigh >> w, vt = gufunc(a, signature=signature, extobj=extobj) >> File >> "/Users/yehp/anaconda3/lib/python3.6/site-packages/numpy/linalg/linalg.py", >> line 95, in _raise_linalgerror_eigenvalues_nonconvergence >> raise LinAlgError("Eigenvalues did not converge") >> numpy.linalg.linalg.LinAlgError: Eigenvalues did not converge >> >> >> Any suggestions? >> >> Thank you. >> >> Ping >> >> _______________________________________________ >> 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... 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