From lists at onerussian.com Mon Aug 1 12:14:15 2016 From: lists at onerussian.com (Yaroslav Halchenko) Date: Mon, 1 Aug 2016 12:14:15 -0400 Subject: [Neuroimaging] Nibabel release imminent In-Reply-To: References: <20160729133544.GI22292@onerussian.com> <20160730004430.GQ22292@onerussian.com> Message-ID: <20160801161415.GC3669@onerussian.com> On Sat, 30 Jul 2016, Matthew Brett wrote: > > some detected changes in behaviour of nibabel are detected within pymvpa > > tests... yet to look in details > > ====================================================================== > > ERROR: test_surf_gifti (mvpa2.tests.test_surfing.SurfTests) > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/testing/tools.py", line 165, in newfunc > > func(*(arg + (filename,)), **kw) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/tests/test_surfing.py", line 1081, in test_surf_gifti > > surf.write(fn, s) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/support/nibabel/surf.py", line 2229, in write > > surf_gifti.write(fn, s, overwrite=overwrite) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/support/nibabel/surf_gifti.py", line 254, in write > > xml = to_xml(s, fn) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/support/nibabel/surf_gifti.py", line 203, in to_xml > > img = to_gifti_image(img) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/support/nibabel/surf_gifti.py", line 162, in to_gifti_image > > arr.num_dim = len(arr.dims) > > AttributeError: can't set attribute > The GiftiDataArray object now has `num_dims` as a property. We could > add a setter that raises an error if the value is not as expected, and > a deprecation warning otherwise - OK with you? sure. I will also fixup pymvpa for that so next release would all be ready ;) Thanks! > > ====================================================================== > > FAIL: mvpa2.tests.test_niftidataset.test_assumptions_on_nibabel_behavior > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest > > self.test(*self.arg) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/testing/tools.py", line 165, in newfunc > > func(*(arg + (filename,)), **kw) > > File "/build/pymvpa2-2.3.1/debian/tmp/usr/lib/python2.7/dist-packages/mvpa2/tests/test_niftidataset.py", line 425, in test_assumptions_on_nibabel_behavior > > assert_equal(slope, 1.0) > > AssertionError: None != 1.0 > Does this one work on current released nibabel? This behavior > changed before version 2 as I remember - the slope and intercept are > recorded as None in the header by default, after reading. oh -- sorry about the noise on this one -- I have missed that I was testing against elderly release (2.3.1) instead of the most recent one (2.5.0) on this one... And that one is all cool ;) -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik From lists at onerussian.com Mon Aug 1 12:15:08 2016 From: lists at onerussian.com (Yaroslav Halchenko) Date: Mon, 1 Aug 2016 12:15:08 -0400 Subject: [Neuroimaging] Nibabel release imminent In-Reply-To: References: <20160729133544.GI22292@onerussian.com> <20160730004430.GQ22292@onerussian.com> Message-ID: <20160801161507.GD3669@onerussian.com> meanwhile have ran/found another fresh one: https://github.com/nipy/nibabel/issues/469 -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik From matthew.brett at gmail.com Sat Aug 6 19:42:44 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 6 Aug 2016 16:42:44 -0700 Subject: [Neuroimaging] Upcoming nibabel 2.1 release - please check Changelog Message-ID: Hi, I've just done the first draft of the Changelog for upcoming 2.1 release of nibabel. It's here : https://github.com/nipy/nibabel/pull/475 Please can y'all have a look and make sure I've credited you and that I haven't missed off anything important? Cheers, Matthew From docpatient at gmail.com Sun Aug 7 22:26:10 2016 From: docpatient at gmail.com (Francesco) Date: Sun, 7 Aug 2016 22:26:10 -0400 Subject: [Neuroimaging] Number of voxels in mask showing connectivity Message-ID: Dear experts how can I do my analysis in Probtrackx using a small (2mm radius) ROI and a cortical mask *to obtain the number of voxels in the cortical mask that are connected to the small ROI? Like in this figure (attached)* *Thank you a lot!* *?* -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen-Shot-2016-08-07-at-9.56.03-PM.jpg Type: image/jpeg Size: 56687 bytes Desc: not available URL: From jevillalonr at gmail.com Mon Aug 8 15:38:47 2016 From: jevillalonr at gmail.com (Julio Villalon) Date: Mon, 8 Aug 2016 12:38:47 -0700 Subject: [Neuroimaging] SIPAIM 2016 - Tandil, Argentina December 5-8, 2016 Message-ID: Hi everyone, SIPAIM is the leading conference in Biomedical Image and Signal processing in Latin America. This year, the conference will be held in Tandil, Argentina, December 5-8. The deadline to submit a 6-page paper in SPIE format is August 22nd. See below for more information. Cheers! Julio Villal?n Imaging Genetics Center University of Southern California *http://www.sipaim.org/ * SIPAIM 2016: International Seminar of Processing and Analysis of Medical Information December 5-8, 2016 | Tandil | Argentina Manuscript submission *deadline* is approaching: *August 1.* Official Website This year the conference will be held in the city of Tandil , Argentina , one of the main tourist centers of the Province of Buenos Aires. Located in the southeast of the Province, the city is well known for its wild scenery, its mountains ranges (the Tandilia hills or Sierras), its peacefulness and its rich variety of locally produced cheese, hams and sausages. Travel & Venue. Abstract and manuscript submissions for SIPAIM 2016 will go through the SPIE Submission and Review System and will be included in the Proceedings of *SPIE Digital Library*, indexed in Scopus among other important databases. SPIE Paper Submission . This is an excellent opportunity to share your original work in the following fields: - Medical and Biomedical Imaging - E-Health - Digital Pathology - Gait Analysis and Biosignals - Representation Based Biosignal Analysis - Analysis of Medical Procedures Through Imaging For more information and a full list of sub-topics please check: Topics Invited Speakers: - *Paul Thompson, Ph.D. | *Laboratory of Neuro-Imaging Institute for Neuroimaging and Informatics Keck School of Medicine of USC.University of Southern California - USA - *Olivier Coulon, Ph.D. | *The CNRS director of research at the 'Institut de Neurosciences de la Timone' (INT), in Marseille, France - *Marius George Linguraru, Ph.D. | *Principal Investigator in the Sheikh Zayed Institute for Children's National Health System. George Washington University - USA. - *Anant Madabhushi, Ph.D. | *Director of the Center for Computational Imaging and Personalized Diagnostics (CCIPD).Case Western Reserve University - USA. - *Petia Radeva, Ph.D. | *Principal Investigator in Barcelona Perceptual Computing Laboratory (BCNPCL).Universitat Aut?noma - Spain Workshops: - *Tutorial 1: *Diagnosis of aortic diseases using Computed Tomography images and deformable surface models | *Dr. Damian Craiem*| Universidad Favaloro - Argentina - *Tutorial 2: *Neural network mapping before and during epileptic seizures in human of intracerebral macro and micro electrodes |*Dr. Silvia Kochen *| CONICET - Argentina - *Tutorial 3: *Eye Cancer Treatment | *Dr. Guillermo Chantada*| Hospital Pediatrico Garrahan - Argentina *Please feel free to circulate this announcement among your colleagues.* We look forward to meeting you in Tandil for SIPAIM 2016. Best regards, SIPAIM 2016 | Organizing Committee -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/octet-stream Size: 119811 bytes Desc: not available URL: From japsai at gmail.com Tue Aug 9 21:07:28 2016 From: japsai at gmail.com (Jasper van den Bosch) Date: Tue, 9 Aug 2016 18:07:28 -0700 Subject: [Neuroimaging] nibabel: add dependency on Mock library? Message-ID: Hi all, I wrote a unit test for the PR linked below, before I found out that Mock is not a nibabel dependency yet. What are your thoughts on including it? https://github.com/nipy/nibabel/pull/478 For examples of unittesting with Mock check out e.g. the Niprov tests; https://github.com/ilogue/niprov/tree/master/tests Jasper @ilogue -- Jasper van den Bosch Postdoctoral Fellow Institute for Learning and Brain Sciences Portage Bay Bldg. Room 366 Box 357988 University of Washington Seattle, WA 98195-7988 Phone: 1-206-685-0361 Fax: 1-206-221-6472 jasperb at uw.edu http://ilabs.washington.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From khamael at gmail.com Wed Aug 10 04:50:05 2016 From: khamael at gmail.com (paulo rodrigues) Date: Wed, 10 Aug 2016 10:50:05 +0200 Subject: [Neuroimaging] Neuroimaging position Message-ID: We are looking for an experienced neuroimaging developer/scientist. You are experienced in volumetric, diffusion, rs-fMRI studies, and are not shy about Python, bash, R or whatever tool fits the work? Do you know the plethora of tools like mrtrix, ANTs, freesurfer, dipy, nipype, ...? The challenge is to develop analysis systems for multidimensional medical datasets. Mint Labs is a cloud computing platform that focus on integrating diverse clinical, imaging, genomic, and other data to better evaluate disease progression and response to interventions. You will start a new project focusing on using these methods to answer some pertinent questions in MR. You thrive in analyzing data, developing pipelines to process imaging data, and integrate multiple data points into meaningful group conclusions? *Objectives of the position * -------------------------- The position hinges on building sophisticated processing pipelines for neuroimaging datasets. Building, improving advanced morphometrics and brain-parcellation techniques in structural MRI, dMRI / fMRI. Support the interaction with several external research partners and clients to develop neuroimaging analysis *About Mint Labs* -------------------------- Mint Labs is a Barcelona based startup building a neuroimaging data analytics cloud-based platform. The system employs software tools to integrate thousands of images and data from a patient and creates a specific detailed 3D map of the brain. We can quantify the effect of the treatment in the damage of the brain and characterise patients for clinical trials. The images are directly sent from the scanners to our servers, and there the data is automatically processed and analysed. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jevillalonr at gmail.com Wed Aug 10 17:46:59 2016 From: jevillalonr at gmail.com (Julio Villalon) Date: Wed, 10 Aug 2016 14:46:59 -0700 Subject: [Neuroimaging] SIPAIM 2016 - Tandil, Argentina December 5-8, 2016 Message-ID: Hi everyone, SIPAIM is the leading conference in Biomedical Image and Signal processing in Latin America. This year, the conference will be held in Tandil, Argentina, December 5-8. The deadline to submit a 6-page paper in SPIE format is August 22nd. See below for more information. Cheers! Julio Villal?n Imaging Genetics Center University of Southern California *http://www.sipaim.org/ * SIPAIM 2016: International Seminar of Processing and Analysis of Medical Information December 5-8, 2016 | Tandil | Argentina Manuscript submission *deadline* is approaching: *August 1.* Official Website This year the conference will be held in the city of Tandil , Argentina , one of the main tourist centers of the Province of Buenos Aires. Located in the southeast of the Province, the city is well known for its wild scenery, its mountains ranges (the Tandilia hills or Sierras), its peacefulness and its rich variety of locally produced cheese, hams and sausages. Travel & Venue. Abstract and manuscript submissions for SIPAIM 2016 will go through the SPIE Submission and Review System and will be included in the Proceedings of *SPIE Digital Library*, indexed in Scopus among other important databases. SPIE Paper Submission . This is an excellent opportunity to share your original work in the following fields: - Medical and Biomedical Imaging - E-Health - Digital Pathology - Gait Analysis and Biosignals - Representation Based Biosignal Analysis - Analysis of Medical Procedures Through Imaging For more information and a full list of sub-topics please check: Topics Invited Speakers: - *Paul Thompson, Ph.D. | *Laboratory of Neuro-Imaging Institute for Neuroimaging and Informatics Keck School of Medicine of USC.University of Southern California - USA - *Olivier Coulon, Ph.D. | *The CNRS director of research at the 'Institut de Neurosciences de la Timone' (INT), in Marseille, France - *Marius George Linguraru, Ph.D. | *Principal Investigator in the Sheikh Zayed Institute for Children's National Health System. George Washington University - USA. - *Anant Madabhushi, Ph.D. | *Director of the Center for Computational Imaging and Personalized Diagnostics (CCIPD).Case Western Reserve University - USA. - *Petia Radeva, Ph.D. | *Principal Investigator in Barcelona Perceptual Computing Laboratory (BCNPCL).Universitat Aut?noma - Spain Workshops: - *Tutorial 1: *Diagnosis of aortic diseases using Computed Tomography images and deformable surface models | *Dr. Damian Craiem*| Universidad Favaloro - Argentina - *Tutorial 2: *Neural network mapping before and during epileptic seizures in human of intracerebral macro and micro electrodes |*Dr. Silvia Kochen *| CONICET - Argentina - *Tutorial 3: *Eye Cancer Treatment | *Dr. Guillermo Chantada*| Hospital Pediatrico Garrahan - Argentina *Please feel free to circulate this announcement among your colleagues.* We look forward to meeting you in Tandil for SIPAIM 2016. Best regards, SIPAIM 2016 | Organizing Committee -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Mon Aug 15 20:48:56 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Mon, 15 Aug 2016 17:48:56 -0700 Subject: [Neuroimaging] Upcoming nibabel 2.1 release - please check Changelog In-Reply-To: References: Message-ID: Hi, On Sat, Aug 6, 2016 at 4:42 PM, Matthew Brett wrote: > Hi, > > I've just done the first draft of the Changelog for upcoming 2.1 > release of nibabel. > > It's here : https://github.com/nipy/nibabel/pull/475 > > Please can y'all have a look and make sure I've credited you and that > I haven't missed off anything important? Last call for checks to Changelog: https://github.com/nipy/nibabel/pull/475 I propose to release nibabel 2.1 with that merged, and this tiny PR that needs a review: https://github.com/nipy/nibabel/pull/481 Any comments / objections? Cheers, Matthew From maxime.descoteaux at gmail.com Thu Aug 18 05:17:07 2016 From: maxime.descoteaux at gmail.com (Maxime Descoteaux) Date: Thu, 18 Aug 2016 11:17:07 +0200 Subject: [Neuroimaging] ISMRM diffusion workshop: -1 month! Message-ID: Dear all, Time is running fast and this is just a kind reminder that the countdown for the ISMRM workshop on breaking the barriers of diffusion MRI has started. The meeting will take place in Lisbon, 11-16 September. Please check http://www.ismrm.org/workshops/Diffusion16/ for program and updates. The registration is still open! However, please note that accommodation at the Sheraton Lisboa hotel is still available but not at the discounted ISMRM rate (all the rooms have gone!). Alternative options can be found at http://www.ismrm.org/workshops/Diffusion16/housing.htm. We are looking forward seeing you there! The organizing team Mara Cercignani, Brighton & Sussex Medical School, Brighton, England, UK Maxime Descoteaux, Sherbrooke University, Sherbrooke, QC, Canada Tim B. Dyrby, Danish Research Centre for Magnetic Resonance, Hvidovre, Denmark Christopher Hess, University of California, San Francisco, CA, USA Alexander Leemans, University Medical Center Utrecht, Utrecht, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.eickhoff at fz-juelich.de Mon Aug 22 06:30:40 2016 From: s.eickhoff at fz-juelich.de (Eickhoff, Simon) Date: Mon, 22 Aug 2016 10:30:40 +0000 Subject: [Neuroimaging] Postdoc / staff-scientist Message-ID: <672934F7DCB66449B220A3A7664839AA62F34808@MBX2010-E01.ad.fz-juelich.de> Dear colleagues We are pleased to announce the following open postdoc / staff-scientist position(s) at the Institute of Neuroscience and Medicine, Research Center J?lich, Germany! The Institute for Neuroscience and Medicine (INM) explores the structure and function of the brain in healthy subjects and in patients with neurological and psychiatric diseases. The Department of Structural and Functional Organisation of the Brain (INM-1; head Professor Katrin Amunts) has a long-standing expertise in mapping brain networks and their inter-individual variability by integrating structure, function, connectivity and behavior. In addition, as a core partner of the Human Brain Project (HBP), we are currently building pipelines for high-throughput neuroimaging analyses and multi-modal brain mapping, enabling population-based descriptions of neurobiology and brain-behavior associations. As part of these endeavors, the INM-1 is currently offering postdoc / staff-scientist positions in neuroimaging to be filled as soon as possible. Working at the interface between methods development, high-performance computing as well as basic and clinical neuroscience, this project focus on multi-modal in-vivo brain parcellation. The key idea of this work is to integrate brain parcellation based on multiple complementary features with in-depth descriptions of the ensuing modules, including inter-individual variability and brain-behavior analysis as well as clinical implications. Hereby we will leverage the available large neuroimaging datasets and high-performance computing capabilities into dynamic multi-modal population-based atlases of structure, function, connectivity and behavior. Together with an interdisciplinary team you will be involved in all research and organization aspects, ranging from data management and methods development to analysis of regional brain organization and distributed networks, as well as the publication of the results. You will also assist in supervising junior (MSc and, in case of a postdoc position, PhD) students. Your profile: * PhD (Neuroscience, Psychology, Computer Science, Engineering or related areas) or Masters degree and relevant work experience * Programming expertise in Python and (ideally) Matlab * Substantial experience in neuroimaging packages such as SPM, FSL, NiPy etc. * In-depth knowledge of spoken and written English, previous publications required for post-doc position * Good interpersonal and organizational skills * High motivation to work in an interdisciplinary environment Our offer: * Work on innovative methods and applications in one of the most dynamic fields of imaging neuroscience, including unique opportunities to pioneer the integration of high-throughput computing and brain atlasing * An interdisciplinary, international research environment on an attractive research campus, ideally situated between the cities of Cologne, D?sseldorf and Aachen * World-class technical facilities, cutting-edge software technologies and fascinating neuroscientific datasets to work with * A wide spectrum of individual training opportunities * At least 2 year full-time position with options for long-term employment * Salary conforming to salary grade E13 of the Collective Agreement for the German Civil Service (TV?D) according to experience The Forschungszentrum J?lich aims to employ more women in this area and therefore particularly welcomes applications from women. We also welcome applications from disabled persons. The position is available immediately and search will continue until a candidate has been selected. For further information or informal inquiries, please contact Professor Simon Eickhoff (s.eickhoff at fz-juelich.de). If this position has raised you interest, please sent your application documents by email to s.eickhoff at fz-juelich.de. =================================== Univ.-Prof. Dr. med. Simon B. Eickhoff Cognitive Neuroscience Group Institute of Clinical Neuroscience and Medical Psychology Heinrich-Heine University D?sseldorf Telefon: +49 211 81 13018 Fax: +49 211 81 13015 eMail: Simon.Eickhoff at uni-duesseldorf.de and Brain Network Modelling Group Institute for Neuroscience and Medicine (INM-1) Research Center J?lich Telefon: +49 2461 61 8609 Fax: +49 2461 61 2820 eMail: S.Eickhoff at fz-juelich.de ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Mon Aug 22 14:39:31 2016 From: arokem at gmail.com (Ariel Rokem) Date: Mon, 22 Aug 2016 11:39:31 -0700 Subject: [Neuroimaging] Multiprocessing the multivoxel fit Message-ID: Hi everyone, Shahnawaz, soon to be a Google Summer of Code alumnus, expressed interest in working on multiprocessing the multivoxel fits in dipy (along the lines of this issue: https://github.com/nipy/dipy/issues/1026). This would be a good time to revisit that issue and make comments if you have any. We've also scheduled a hang-out to discuss this: next Monday (August 29th), at 11 AM PST. If you are interested in joining the conversation, please let me know, so that I can add you to that hang-out. Cheers, Ariel -------------- next part -------------- An HTML attachment was scrubbed... URL: From garyfallidis at gmail.com Mon Aug 22 17:27:08 2016 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Mon, 22 Aug 2016 21:27:08 +0000 Subject: [Neuroimaging] Multiprocessing the multivoxel fit In-Reply-To: References: Message-ID: I want to attend but the proposed time is not good can you suggest an alternative time or setup a doodle? On Mon, Aug 22, 2016, 2:45 PM Ariel Rokem wrote: > Hi everyone, > > Shahnawaz, soon to be a Google Summer of Code alumnus, expressed interest > in working on multiprocessing the multivoxel fits in dipy (along the lines > of this issue: https://github.com/nipy/dipy/issues/1026). This would be a > good time to revisit that issue and make comments if you have any. We've > also scheduled a hang-out to discuss this: next Monday (August 29th), at 11 > AM PST. If you are interested in joining the conversation, please let me > know, so that I can add you to that hang-out. > > Cheers, > > Ariel > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Mon Aug 22 19:40:00 2016 From: arokem at gmail.com (Ariel Rokem) Date: Mon, 22 Aug 2016 16:40:00 -0700 Subject: [Neuroimaging] Multiprocessing the multivoxel fit In-Reply-To: References: Message-ID: Hi Eleftherios, On Mon, Aug 22, 2016 at 2:27 PM, Eleftherios Garyfallidis < garyfallidis at gmail.com> wrote: > I want to attend but the proposed time is not good can you suggest an > alternative time or setup a doodle? > OK -- here is a poll with a few times that week: http://whenisgood.net/3wm744k > On Mon, Aug 22, 2016, 2:45 PM Ariel Rokem wrote: > >> Hi everyone, >> >> Shahnawaz, soon to be a Google Summer of Code alumnus, expressed interest >> in working on multiprocessing the multivoxel fits in dipy (along the lines >> of this issue: https://github.com/nipy/dipy/issues/1026). This would be >> a good time to revisit that issue and make comments if you have any. We've >> also scheduled a hang-out to discuss this: next Monday (August 29th), at 11 >> AM PST. If you are interested in joining the conversation, please let me >> know, so that I can add you to that hang-out. >> >> Cheers, >> >> Ariel >> _______________________________________________ >> 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 Mon Aug 22 23:40:10 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Mon, 22 Aug 2016 20:40:10 -0700 Subject: [Neuroimaging] Nibabel release 2.1 Message-ID: Hi, Welcome to the new 2.1 release of nibabel, the result of six months of hard work. Many thanks in particular to Ben, Marc-Alexandre C?t?, Chris Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large contributions to this release. A special shout-out to those of you doing code-reviews, it's essential work, and not enough rewarded. A special-special shout-out to Chris, Eric and Ben, and much thanks to Jean-Christophe Houde, Bago Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work reviewing Marc-Alexandre C?t?'s huge streamline format PR (see below). Here's the Changelog for your viewing pleasure: Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan Gerhard (SG) and Eric Larson (EL). References like "pr/298" refer to github pull request numbers. 2.1 (Monday 22 August 2016) =========================== New features ------------ * New API for managing streamlines and their different file formats. This adds a new module ``nibabel.streamlines`` that will eventually deprecate the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC, reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean, MB); * A prototype image viewer using matplotlib (pr/404) (EL, based on a proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB); * Functions for image resampling and smoothing using scipy ndimage (pr/255) (MB, reviewed by EL, BC); * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, reviewed by BC); * Read and write support for DICOM tags in NIfTI Extended Header using pydicom (pr/296) (Eric Kastman). Enhancements ------------ * Extensions to FreeSurfer module to fix reading and writing of FreeSurfer geometry data (pr/460) (Alexandre Gramfort, Jaakko Lepp?kangas, reviewed by EL, CM, MB); * Various improvements to PAR / REC handling by Gregory R. Lee: supporting multiple TR values (pr/429); output of volume labels (pr/427); fix for some diffusion files (pr/426); option for more sophisticated sorting of volumes (pr/409); * Original trackvis reader will now allow final streamline to have fewer points than the number declared in the header, with ``strict=False`` argument to ``read`` function; * Helper function to return voxel sizes from an affine matrix (pr/413); * Fixes to DICOM multiframe reading to avoid assumptions on the position of the multiframe index (pr/439) (Eric M. Baker); * More robust handling of "CSA" private information in DICOM files (pr/393) (Brendan Moloney); * More explicit error when trying to read image from non-existent file (pr/455) (Ariel Rokem); * Extension to `nib-ls` command to show image statistics (pr/437) and other header files (pr/348) (Yarik Halchenko). Bug fixes --------- * Fixes to rotation order to generate affine matrices of PAR / REC files (MB, Gregory R Lee). Maintenance ----------- * Dropped support for Pythons 2.6 and 3.2; * Comprehensive refactor and generalization of surface / GIFTI file support with improved API and extended tests (pr/352-355, pr/360, pr/365, pr/403) (BC, reviewed by CM, MB); * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM); * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem); * Fix shebang lines in scripts for correct install into virtualenvs via pip (pr/434); * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility (CM, Ariel Rokem, MB); * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB); * New decorator to specify start and end versions for deprecation warnings (MB, reviewed by CM); * Write qform affine matrix to NIfTI images output by ``parrec2nii`` (pr/478) (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB). API changes and deprecations ---------------------------- * Minor API breakage in original (rather than new) trackvis reader. We are now raising a ``DataError`` if there are too few streamlines in the file, instead of a ``HeaderError``. We are raising a ``DataError`` if the track is truncated when ``strict=True`` (the default), rather than a ``TypeError`` when trying to create the points array. * Change sform code that ``parrec2nii`` script writes to NIfTI images; change from 2 ("aligned") to 1 ("scanner"); * Deprecation of ``get_header``, ``get_affine`` method of image objects for removal in version 4.0; * Removed broken ``from_filespec`` method from image objects, and deprecated ``from_filespec`` method of ECAT image objects for removal in 4.0; * Deprecation of ``class_map`` instance in ``imageclasses`` module in favor of new image class attributes, for removal in 4.0; * Deprecation of ``ext_map`` instance in ``imageclasses`` module in favor of new image loading API, for removal in 4.0; * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for removal in 4.0; * Deprecation of ``BinOpener`` class in favor of more generic ``Opener`` class, for removal in 4.0; * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and ``get_rgba``; ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``, ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, ``set_meta``. All these deprecated in favor of corresponding properties, for removal in 4.0; * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of nibabel ``load`` and ``save`` functions, for removal in 4.0; * Deprecation of ``gifti.data_tag`` function, for removal in 4.0; * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new error when trying to set invalid values for ``num_dim``. We will remove write-access in 4.0; * Deprecation of ``GiftiDataArray.from_array`` in favor of ``GiftiDataArray`` constructor, for removal in 4.0; * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` methods in favor of ``to_xml`` method, for removal in 4.0; * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of ``GiftiImageParser``, for removal in 4.0; * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in favor of ``GiftiImageParser.parse`` method, for removal in 4.0; * Deprecation of ``loadsave`` functions ``guessed_image_type`` and ``which_analyze_type``, in favor of new API where each image class tests the file for compatibility during load, for removal in 4.0; NGUNS, on behalf of all Nibabelers, Matthew From jean.christophe.houde at gmail.com Mon Aug 22 23:43:46 2016 From: jean.christophe.houde at gmail.com (Jean-Christophe Houde) Date: Mon, 22 Aug 2016 23:43:46 -0400 Subject: [Neuroimaging] Nibabel release 2.1 In-Reply-To: References: Message-ID: Congratulations on the hard work! 2016-08-22 23:40 GMT-04:00 Matthew Brett : > Hi, > > Welcome to the new 2.1 release of nibabel, the result of six months of > hard work. > > Many thanks in particular to Ben, Marc-Alexandre C?t?, Chris > Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large > contributions to this release. > > A special shout-out to those of you doing code-reviews, it's essential > work, and not enough rewarded. A special-special shout-out to Chris, > Eric and Ben, and much thanks to Jean-Christophe Houde, Bago > Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work > reviewing Marc-Alexandre C?t?'s huge streamline format PR (see below). > > Here's the Changelog for your viewing pleasure: > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke > (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), > Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > 2.1 (Monday 22 August 2016) > =========================== > > New features > ------------ > > * New API for managing streamlines and their different file formats. This > adds a new module ``nibabel.streamlines`` that will eventually deprecate > the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC, > reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios > Garyfallidis, Samuel St-Jean, MB); > * A prototype image viewer using matplotlib (pr/404) (EL, based on a > proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB); > * Functions for image resampling and smoothing using scipy ndimage (pr/255) > (MB, reviewed by EL, BC); > * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, > reviewed > by BC); > * Read and write support for DICOM tags in NIfTI Extended Header using > pydicom (pr/296) (Eric Kastman). > > Enhancements > ------------ > > * Extensions to FreeSurfer module to fix reading and writing of FreeSurfer > geometry data (pr/460) (Alexandre Gramfort, Jaakko Lepp?kangas, reviewed > by EL, CM, MB); > * Various improvements to PAR / REC handling by Gregory R. Lee: supporting > multiple TR values (pr/429); output of volume labels (pr/427); fix for > some diffusion files (pr/426); option for more sophisticated sorting of > volumes (pr/409); > * Original trackvis reader will now allow final streamline to have fewer > points than the number declared in the header, with ``strict=False`` > argument to ``read`` function; > * Helper function to return voxel sizes from an affine matrix (pr/413); > * Fixes to DICOM multiframe reading to avoid assumptions on the position of > the multiframe index (pr/439) (Eric M. Baker); > * More robust handling of "CSA" private information in DICOM files (pr/393) > (Brendan Moloney); > * More explicit error when trying to read image from non-existent file > (pr/455) (Ariel Rokem); > * Extension to `nib-ls` command to show image statistics (pr/437) and other > header files (pr/348) (Yarik Halchenko). > > Bug fixes > --------- > > * Fixes to rotation order to generate affine matrices of PAR / REC files > (MB, > Gregory R Lee). > > Maintenance > ----------- > > * Dropped support for Pythons 2.6 and 3.2; > * Comprehensive refactor and generalization of surface / GIFTI file support > with improved API and extended tests (pr/352-355, pr/360, pr/365, pr/403) > (BC, reviewed by CM, MB); > * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM); > * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem); > * Fix shebang lines in scripts for correct install into virtualenvs via pip > (pr/434); > * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility (CM, > Ariel Rokem, MB); > * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB); > * New decorator to specify start and end versions for deprecation warnings > (MB, reviewed by CM); > * Write qform affine matrix to NIfTI images output by ``parrec2nii`` > (pr/478) > (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB). > > API changes and deprecations > ---------------------------- > > * Minor API breakage in original (rather than new) trackvis reader. We are > now > raising a ``DataError`` if there are too few streamlines in the file, > instead of a ``HeaderError``. We are raising a ``DataError`` if the > track > is truncated when ``strict=True`` (the default), rather than a > ``TypeError`` > when trying to create the points array. > * Change sform code that ``parrec2nii`` script writes to NIfTI images; > change > from 2 ("aligned") to 1 ("scanner"); > * Deprecation of ``get_header``, ``get_affine`` method of image objects for > removal in version 4.0; > * Removed broken ``from_filespec`` method from image objects, and > deprecated > ``from_filespec`` method of ECAT image objects for removal in 4.0; > * Deprecation of ``class_map`` instance in ``imageclasses`` module in > favor of > new image class attributes, for removal in 4.0; > * Deprecation of ``ext_map`` instance in ``imageclasses`` module in favor > of > new image loading API, for removal in 4.0; > * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for > removal > in 4.0; > * Deprecation of ``BinOpener`` class in favor of more generic ``Opener`` > class, for removal in 4.0; > * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and > ``get_rgba``; > ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``, > ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, ``set_meta``. > All > these deprecated in favor of corresponding properties, for removal in > 4.0; > * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of > nibabel ``load`` and ``save`` functions, for removal in 4.0; > * Deprecation of ``gifti.data_tag`` function, for removal in 4.0; > * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new error > when trying to set invalid values for ``num_dim``. We will remove > write-access in 4.0; > * Deprecation of ``GiftiDataArray.from_array`` in favor of > ``GiftiDataArray`` > constructor, for removal in 4.0; > * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` methods > in > favor of ``to_xml`` method, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of > ``GiftiImageParser``, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in favor > of > ``GiftiImageParser.parse`` method, for removal in 4.0; > * Deprecation of ``loadsave`` functions ``guessed_image_type`` and > ``which_analyze_type``, in favor of new API where each image class tests > the > file for compatibility during load, for removal in 4.0; > > NGUNS, on behalf of all Nibabelers, > > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Tue Aug 23 14:26:57 2016 From: arokem at gmail.com (Ariel Rokem) Date: Tue, 23 Aug 2016 11:26:57 -0700 Subject: [Neuroimaging] Multiprocessing the multivoxel fit In-Reply-To: References: Message-ID: Clarification: On Mon, Aug 22, 2016 at 4:40 PM, Ariel Rokem wrote: > Hi Eleftherios, > > On Mon, Aug 22, 2016 at 2:27 PM, Eleftherios Garyfallidis < > garyfallidis at gmail.com> wrote: > >> I want to attend but the proposed time is not good can you suggest an >> alternative time or setup a doodle? >> > > OK -- here is a poll with a few times that week: http://whenisgood.net/ > 3wm744k > All times are PST. Cheers, Ariel > > > >> On Mon, Aug 22, 2016, 2:45 PM Ariel Rokem wrote: >> >>> Hi everyone, >>> >>> Shahnawaz, soon to be a Google Summer of Code alumnus, expressed >>> interest in working on multiprocessing the multivoxel fits in dipy (along >>> the lines of this issue: https://github.com/nipy/dipy/issues/1026). >>> This would be a good time to revisit that issue and make comments if you >>> have any. We've also scheduled a hang-out to discuss this: next Monday >>> (August 29th), at 11 AM PST. If you are interested in joining the >>> conversation, please let me know, so that I can add you to that hang-out. >>> >>> Cheers, >>> >>> Ariel >>> _______________________________________________ >>> 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 bertrand.thirion at inria.fr Tue Aug 23 15:38:36 2016 From: bertrand.thirion at inria.fr (bthirion) Date: Tue, 23 Aug 2016 21:38:36 +0200 Subject: [Neuroimaging] Nibabel release 2.1 In-Reply-To: References: Message-ID: Congratulations ! Bertrand On 23/08/2016 05:40, Matthew Brett wrote: > Hi, > > Welcome to the new 2.1 release of nibabel, the result of six months of > hard work. > > Many thanks in particular to Ben, Marc-Alexandre C?t?, Chris > Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large > contributions to this release. > > A special shout-out to those of you doing code-reviews, it's essential > work, and not enough rewarded. A special-special shout-out to Chris, > Eric and Ben, and much thanks to Jean-Christophe Houde, Bago > Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work > reviewing Marc-Alexandre C?t?'s huge streamline format PR (see below). > > Here's the Changelog for your viewing pleasure: > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > 2.1 (Monday 22 August 2016) > =========================== > > New features > ------------ > > * New API for managing streamlines and their different file formats. This > adds a new module ``nibabel.streamlines`` that will eventually deprecate > the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC, > reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios > Garyfallidis, Samuel St-Jean, MB); > * A prototype image viewer using matplotlib (pr/404) (EL, based on a > proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB); > * Functions for image resampling and smoothing using scipy ndimage (pr/255) > (MB, reviewed by EL, BC); > * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, reviewed > by BC); > * Read and write support for DICOM tags in NIfTI Extended Header using > pydicom (pr/296) (Eric Kastman). > > Enhancements > ------------ > > * Extensions to FreeSurfer module to fix reading and writing of FreeSurfer > geometry data (pr/460) (Alexandre Gramfort, Jaakko Lepp?kangas, reviewed > by EL, CM, MB); > * Various improvements to PAR / REC handling by Gregory R. Lee: supporting > multiple TR values (pr/429); output of volume labels (pr/427); fix for > some diffusion files (pr/426); option for more sophisticated sorting of > volumes (pr/409); > * Original trackvis reader will now allow final streamline to have fewer > points than the number declared in the header, with ``strict=False`` > argument to ``read`` function; > * Helper function to return voxel sizes from an affine matrix (pr/413); > * Fixes to DICOM multiframe reading to avoid assumptions on the position of > the multiframe index (pr/439) (Eric M. Baker); > * More robust handling of "CSA" private information in DICOM files (pr/393) > (Brendan Moloney); > * More explicit error when trying to read image from non-existent file > (pr/455) (Ariel Rokem); > * Extension to `nib-ls` command to show image statistics (pr/437) and other > header files (pr/348) (Yarik Halchenko). > > Bug fixes > --------- > > * Fixes to rotation order to generate affine matrices of PAR / REC files (MB, > Gregory R Lee). > > Maintenance > ----------- > > * Dropped support for Pythons 2.6 and 3.2; > * Comprehensive refactor and generalization of surface / GIFTI file support > with improved API and extended tests (pr/352-355, pr/360, pr/365, pr/403) > (BC, reviewed by CM, MB); > * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM); > * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem); > * Fix shebang lines in scripts for correct install into virtualenvs via pip > (pr/434); > * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility (CM, > Ariel Rokem, MB); > * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB); > * New decorator to specify start and end versions for deprecation warnings > (MB, reviewed by CM); > * Write qform affine matrix to NIfTI images output by ``parrec2nii`` (pr/478) > (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB). > > API changes and deprecations > ---------------------------- > > * Minor API breakage in original (rather than new) trackvis reader. We are now > raising a ``DataError`` if there are too few streamlines in the file, > instead of a ``HeaderError``. We are raising a ``DataError`` if the track > is truncated when ``strict=True`` (the default), rather than a ``TypeError`` > when trying to create the points array. > * Change sform code that ``parrec2nii`` script writes to NIfTI images; change > from 2 ("aligned") to 1 ("scanner"); > * Deprecation of ``get_header``, ``get_affine`` method of image objects for > removal in version 4.0; > * Removed broken ``from_filespec`` method from image objects, and deprecated > ``from_filespec`` method of ECAT image objects for removal in 4.0; > * Deprecation of ``class_map`` instance in ``imageclasses`` module in favor of > new image class attributes, for removal in 4.0; > * Deprecation of ``ext_map`` instance in ``imageclasses`` module in favor of > new image loading API, for removal in 4.0; > * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for removal > in 4.0; > * Deprecation of ``BinOpener`` class in favor of more generic ``Opener`` > class, for removal in 4.0; > * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and ``get_rgba``; > ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``, > ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, ``set_meta``. All > these deprecated in favor of corresponding properties, for removal in 4.0; > * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of > nibabel ``load`` and ``save`` functions, for removal in 4.0; > * Deprecation of ``gifti.data_tag`` function, for removal in 4.0; > * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new error > when trying to set invalid values for ``num_dim``. We will remove > write-access in 4.0; > * Deprecation of ``GiftiDataArray.from_array`` in favor of ``GiftiDataArray`` > constructor, for removal in 4.0; > * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` methods in > favor of ``to_xml`` method, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of > ``GiftiImageParser``, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in favor of > ``GiftiImageParser.parse`` method, for removal in 4.0; > * Deprecation of ``loadsave`` functions ``guessed_image_type`` and > ``which_analyze_type``, in favor of new API where each image class tests the > file for compatibility during load, for removal in 4.0; > > NGUNS, on behalf of all Nibabelers, > > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging From jbpoline at gmail.com Wed Aug 24 04:51:36 2016 From: jbpoline at gmail.com (JB Poline) Date: Wed, 24 Aug 2016 01:51:36 -0700 Subject: [Neuroimaging] Nibabel release 2.1 In-Reply-To: References: Message-ID: Thanks a lot for this JB On 22 August 2016 at 20:40, Matthew Brett wrote: > Hi, > > Welcome to the new 2.1 release of nibabel, the result of six months of > hard work. > > Many thanks in particular to Ben, Marc-Alexandre C?t?, Chris > Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large > contributions to this release. > > A special shout-out to those of you doing code-reviews, it's essential > work, and not enough rewarded. A special-special shout-out to Chris, > Eric and Ben, and much thanks to Jean-Christophe Houde, Bago > Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work > reviewing Marc-Alexandre C?t?'s huge streamline format PR (see below). > > Here's the Changelog for your viewing pleasure: > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > 2.1 (Monday 22 August 2016) > =========================== > > New features > ------------ > > * New API for managing streamlines and their different file formats. This > adds a new module ``nibabel.streamlines`` that will eventually deprecate > the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC, > reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios > Garyfallidis, Samuel St-Jean, MB); > * A prototype image viewer using matplotlib (pr/404) (EL, based on a > proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB); > * Functions for image resampling and smoothing using scipy ndimage (pr/255) > (MB, reviewed by EL, BC); > * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, reviewed > by BC); > * Read and write support for DICOM tags in NIfTI Extended Header using > pydicom (pr/296) (Eric Kastman). > > Enhancements > ------------ > > * Extensions to FreeSurfer module to fix reading and writing of FreeSurfer > geometry data (pr/460) (Alexandre Gramfort, Jaakko Lepp?kangas, reviewed > by EL, CM, MB); > * Various improvements to PAR / REC handling by Gregory R. Lee: supporting > multiple TR values (pr/429); output of volume labels (pr/427); fix for > some diffusion files (pr/426); option for more sophisticated sorting of > volumes (pr/409); > * Original trackvis reader will now allow final streamline to have fewer > points than the number declared in the header, with ``strict=False`` > argument to ``read`` function; > * Helper function to return voxel sizes from an affine matrix (pr/413); > * Fixes to DICOM multiframe reading to avoid assumptions on the position of > the multiframe index (pr/439) (Eric M. Baker); > * More robust handling of "CSA" private information in DICOM files (pr/393) > (Brendan Moloney); > * More explicit error when trying to read image from non-existent file > (pr/455) (Ariel Rokem); > * Extension to `nib-ls` command to show image statistics (pr/437) and other > header files (pr/348) (Yarik Halchenko). > > Bug fixes > --------- > > * Fixes to rotation order to generate affine matrices of PAR / REC files (MB, > Gregory R Lee). > > Maintenance > ----------- > > * Dropped support for Pythons 2.6 and 3.2; > * Comprehensive refactor and generalization of surface / GIFTI file support > with improved API and extended tests (pr/352-355, pr/360, pr/365, pr/403) > (BC, reviewed by CM, MB); > * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM); > * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem); > * Fix shebang lines in scripts for correct install into virtualenvs via pip > (pr/434); > * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility (CM, > Ariel Rokem, MB); > * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB); > * New decorator to specify start and end versions for deprecation warnings > (MB, reviewed by CM); > * Write qform affine matrix to NIfTI images output by ``parrec2nii`` (pr/478) > (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB). > > API changes and deprecations > ---------------------------- > > * Minor API breakage in original (rather than new) trackvis reader. We are now > raising a ``DataError`` if there are too few streamlines in the file, > instead of a ``HeaderError``. We are raising a ``DataError`` if the track > is truncated when ``strict=True`` (the default), rather than a ``TypeError`` > when trying to create the points array. > * Change sform code that ``parrec2nii`` script writes to NIfTI images; change > from 2 ("aligned") to 1 ("scanner"); > * Deprecation of ``get_header``, ``get_affine`` method of image objects for > removal in version 4.0; > * Removed broken ``from_filespec`` method from image objects, and deprecated > ``from_filespec`` method of ECAT image objects for removal in 4.0; > * Deprecation of ``class_map`` instance in ``imageclasses`` module in favor of > new image class attributes, for removal in 4.0; > * Deprecation of ``ext_map`` instance in ``imageclasses`` module in favor of > new image loading API, for removal in 4.0; > * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for removal > in 4.0; > * Deprecation of ``BinOpener`` class in favor of more generic ``Opener`` > class, for removal in 4.0; > * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and ``get_rgba``; > ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``, > ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, ``set_meta``. All > these deprecated in favor of corresponding properties, for removal in 4.0; > * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of > nibabel ``load`` and ``save`` functions, for removal in 4.0; > * Deprecation of ``gifti.data_tag`` function, for removal in 4.0; > * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new error > when trying to set invalid values for ``num_dim``. We will remove > write-access in 4.0; > * Deprecation of ``GiftiDataArray.from_array`` in favor of ``GiftiDataArray`` > constructor, for removal in 4.0; > * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` methods in > favor of ``to_xml`` method, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of > ``GiftiImageParser``, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in favor of > ``GiftiImageParser.parse`` method, for removal in 4.0; > * Deprecation of ``loadsave`` functions ``guessed_image_type`` and > ``which_analyze_type``, in favor of new API where each image class tests the > file for compatibility during load, for removal in 4.0; > > NGUNS, on behalf of all Nibabelers, > > Matthew > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging From krzysztof.gorgolewski at gmail.com Wed Aug 24 06:48:58 2016 From: krzysztof.gorgolewski at gmail.com (Chris Gorgolewski) Date: Wed, 24 Aug 2016 03:48:58 -0700 Subject: [Neuroimaging] Nibabel release 2.1 In-Reply-To: References: Message-ID: Congrats! On Aug 24, 2016 4:52 AM, "JB Poline" wrote: > Thanks a lot for this > JB > > On 22 August 2016 at 20:40, Matthew Brett wrote: > > Hi, > > > > Welcome to the new 2.1 release of nibabel, the result of six months of > > hard work. > > > > Many thanks in particular to Ben, Marc-Alexandre C?t?, Chris > > Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large > > contributions to this release. > > > > A special shout-out to those of you doing code-reviews, it's essential > > work, and not enough rewarded. A special-special shout-out to Chris, > > Eric and Ben, and much thanks to Jean-Christophe Houde, Bago > > Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work > > reviewing Marc-Alexandre C?t?'s huge streamline format PR (see below). > > > > Here's the Changelog for your viewing pleasure: > > > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael > Hanke (MH) > > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), > Stephan > > Gerhard (SG) and Eric Larson (EL). > > > > References like "pr/298" refer to github pull request numbers. > > > > 2.1 (Monday 22 August 2016) > > =========================== > > > > New features > > ------------ > > > > * New API for managing streamlines and their different file formats. This > > adds a new module ``nibabel.streamlines`` that will eventually > deprecate > > the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC, > > reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios > > Garyfallidis, Samuel St-Jean, MB); > > * A prototype image viewer using matplotlib (pr/404) (EL, based on a > > proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB); > > * Functions for image resampling and smoothing using scipy ndimage > (pr/255) > > (MB, reviewed by EL, BC); > > * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, > reviewed > > by BC); > > * Read and write support for DICOM tags in NIfTI Extended Header using > > pydicom (pr/296) (Eric Kastman). > > > > Enhancements > > ------------ > > > > * Extensions to FreeSurfer module to fix reading and writing of > FreeSurfer > > geometry data (pr/460) (Alexandre Gramfort, Jaakko Lepp?kangas, > reviewed > > by EL, CM, MB); > > * Various improvements to PAR / REC handling by Gregory R. Lee: > supporting > > multiple TR values (pr/429); output of volume labels (pr/427); fix for > > some diffusion files (pr/426); option for more sophisticated sorting of > > volumes (pr/409); > > * Original trackvis reader will now allow final streamline to have fewer > > points than the number declared in the header, with ``strict=False`` > > argument to ``read`` function; > > * Helper function to return voxel sizes from an affine matrix (pr/413); > > * Fixes to DICOM multiframe reading to avoid assumptions on the position > of > > the multiframe index (pr/439) (Eric M. Baker); > > * More robust handling of "CSA" private information in DICOM files > (pr/393) > > (Brendan Moloney); > > * More explicit error when trying to read image from non-existent file > > (pr/455) (Ariel Rokem); > > * Extension to `nib-ls` command to show image statistics (pr/437) and > other > > header files (pr/348) (Yarik Halchenko). > > > > Bug fixes > > --------- > > > > * Fixes to rotation order to generate affine matrices of PAR / REC files > (MB, > > Gregory R Lee). > > > > Maintenance > > ----------- > > > > * Dropped support for Pythons 2.6 and 3.2; > > * Comprehensive refactor and generalization of surface / GIFTI file > support > > with improved API and extended tests (pr/352-355, pr/360, pr/365, > pr/403) > > (BC, reviewed by CM, MB); > > * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM); > > * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem); > > * Fix shebang lines in scripts for correct install into virtualenvs via > pip > > (pr/434); > > * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility > (CM, > > Ariel Rokem, MB); > > * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB); > > * New decorator to specify start and end versions for deprecation > warnings > > (MB, reviewed by CM); > > * Write qform affine matrix to NIfTI images output by ``parrec2nii`` > (pr/478) > > (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB). > > > > API changes and deprecations > > ---------------------------- > > > > * Minor API breakage in original (rather than new) trackvis reader. We > are now > > raising a ``DataError`` if there are too few streamlines in the file, > > instead of a ``HeaderError``. We are raising a ``DataError`` if the > track > > is truncated when ``strict=True`` (the default), rather than a > ``TypeError`` > > when trying to create the points array. > > * Change sform code that ``parrec2nii`` script writes to NIfTI images; > change > > from 2 ("aligned") to 1 ("scanner"); > > * Deprecation of ``get_header``, ``get_affine`` method of image objects > for > > removal in version 4.0; > > * Removed broken ``from_filespec`` method from image objects, and > deprecated > > ``from_filespec`` method of ECAT image objects for removal in 4.0; > > * Deprecation of ``class_map`` instance in ``imageclasses`` module in > favor of > > new image class attributes, for removal in 4.0; > > * Deprecation of ``ext_map`` instance in ``imageclasses`` module in > favor of > > new image loading API, for removal in 4.0; > > * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for > removal > > in 4.0; > > * Deprecation of ``BinOpener`` class in favor of more generic ``Opener`` > > class, for removal in 4.0; > > * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and > ``get_rgba``; > > ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``, > > ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, > ``set_meta``. All > > these deprecated in favor of corresponding properties, for removal in > 4.0; > > * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of > > nibabel ``load`` and ``save`` functions, for removal in 4.0; > > * Deprecation of ``gifti.data_tag`` function, for removal in 4.0; > > * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new > error > > when trying to set invalid values for ``num_dim``. We will remove > > write-access in 4.0; > > * Deprecation of ``GiftiDataArray.from_array`` in favor of > ``GiftiDataArray`` > > constructor, for removal in 4.0; > > * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` > methods in > > favor of ``to_xml`` method, for removal in 4.0; > > * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of > > ``GiftiImageParser``, for removal in 4.0; > > * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in > favor of > > ``GiftiImageParser.parse`` method, for removal in 4.0; > > * Deprecation of ``loadsave`` functions ``guessed_image_type`` and > > ``which_analyze_type``, in favor of new API where each image class > tests the > > file for compatibility during load, for removal in 4.0; > > > > NGUNS, on behalf of all Nibabelers, > > > > Matthew > > _______________________________________________ > > 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 j.schreiber at fz-juelich.de Wed Aug 24 07:42:48 2016 From: j.schreiber at fz-juelich.de (Jan Schreiber) Date: Wed, 24 Aug 2016 13:42:48 +0200 Subject: [Neuroimaging] Nibabel release 2.1 In-Reply-To: References: Message-ID: <57BD8838.3000909@fz-juelich.de> NiBabel is awesome :-) Thanks! -Jan On 08/23/16 05:40, Matthew Brett wrote: > Hi, > > Welcome to the new 2.1 release of nibabel, the result of six months of > hard work. > > Many thanks in particular to Ben, Marc-Alexandre C?t?, Chris > Markiewicz, Eric Larson, Gregory Lee and Erik Kastman for their large > contributions to this release. > > A special shout-out to those of you doing code-reviews, it's essential > work, and not enough rewarded. A special-special shout-out to Chris, > Eric and Ben, and much thanks to Jean-Christophe Houde, Bago > Amirbekian, Eleftherios Garyfallidis, Samuel St-Jean for their work > reviewing Marc-Alexandre C?t?'s huge streamline format PR (see below). > > Here's the Changelog for your viewing pleasure: > > Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH) > Ben Cipollini (BC), Marc-Alexandre C?t? (MC), Chris Markiewicz (CM), Stephan > Gerhard (SG) and Eric Larson (EL). > > References like "pr/298" refer to github pull request numbers. > > 2.1 (Monday 22 August 2016) > =========================== > > New features > ------------ > > * New API for managing streamlines and their different file formats. This > adds a new module ``nibabel.streamlines`` that will eventually deprecate > the current trackvis reader found in ``nibabel.trackvis`` (pr/391) (MC, > reviewed by Jean-Christophe Houde, Bago Amirbekian, Eleftherios > Garyfallidis, Samuel St-Jean, MB); > * A prototype image viewer using matplotlib (pr/404) (EL, based on a > proto-prototype by Paul Ivanov) (Reviewed by Gregory R. Lee, MB); > * Functions for image resampling and smoothing using scipy ndimage (pr/255) > (MB, reviewed by EL, BC); > * Add ability to write FreeSurfer morphology data (pr/414) (CM, BC, reviewed > by BC); > * Read and write support for DICOM tags in NIfTI Extended Header using > pydicom (pr/296) (Eric Kastman). > > Enhancements > ------------ > > * Extensions to FreeSurfer module to fix reading and writing of FreeSurfer > geometry data (pr/460) (Alexandre Gramfort, Jaakko Lepp?kangas, reviewed > by EL, CM, MB); > * Various improvements to PAR / REC handling by Gregory R. Lee: supporting > multiple TR values (pr/429); output of volume labels (pr/427); fix for > some diffusion files (pr/426); option for more sophisticated sorting of > volumes (pr/409); > * Original trackvis reader will now allow final streamline to have fewer > points than the number declared in the header, with ``strict=False`` > argument to ``read`` function; > * Helper function to return voxel sizes from an affine matrix (pr/413); > * Fixes to DICOM multiframe reading to avoid assumptions on the position of > the multiframe index (pr/439) (Eric M. Baker); > * More robust handling of "CSA" private information in DICOM files (pr/393) > (Brendan Moloney); > * More explicit error when trying to read image from non-existent file > (pr/455) (Ariel Rokem); > * Extension to `nib-ls` command to show image statistics (pr/437) and other > header files (pr/348) (Yarik Halchenko). > > Bug fixes > --------- > > * Fixes to rotation order to generate affine matrices of PAR / REC files (MB, > Gregory R Lee). > > Maintenance > ----------- > > * Dropped support for Pythons 2.6 and 3.2; > * Comprehensive refactor and generalization of surface / GIFTI file support > with improved API and extended tests (pr/352-355, pr/360, pr/365, pr/403) > (BC, reviewed by CM, MB); > * Refactor of image classes (pr/328, pr/329) (BC, reviewed by CM); > * Better Appveyor testing on new Python versions (pr/446) (Ariel Rokem); > * Fix shebang lines in scripts for correct install into virtualenvs via pip > (pr/434); > * Various fixes for numpy, matplotlib, and PIL / Pillow compatibility (CM, > Ariel Rokem, MB); > * Improved test framework for warnings (pr/345) (BC, reviewed by CM, MB); > * New decorator to specify start and end versions for deprecation warnings > (MB, reviewed by CM); > * Write qform affine matrix to NIfTI images output by ``parrec2nii`` (pr/478) > (Jasper J.F. van den Bosch, reviewed by Gregory R. Lee, MB). > > API changes and deprecations > ---------------------------- > > * Minor API breakage in original (rather than new) trackvis reader. We are now > raising a ``DataError`` if there are too few streamlines in the file, > instead of a ``HeaderError``. We are raising a ``DataError`` if the track > is truncated when ``strict=True`` (the default), rather than a ``TypeError`` > when trying to create the points array. > * Change sform code that ``parrec2nii`` script writes to NIfTI images; change > from 2 ("aligned") to 1 ("scanner"); > * Deprecation of ``get_header``, ``get_affine`` method of image objects for > removal in version 4.0; > * Removed broken ``from_filespec`` method from image objects, and deprecated > ``from_filespec`` method of ECAT image objects for removal in 4.0; > * Deprecation of ``class_map`` instance in ``imageclasses`` module in favor of > new image class attributes, for removal in 4.0; > * Deprecation of ``ext_map`` instance in ``imageclasses`` module in favor of > new image loading API, for removal in 4.0; > * Deprecation of ``Header`` class in favor of ``SpatialHeader``, for removal > in 4.0; > * Deprecation of ``BinOpener`` class in favor of more generic ``Opener`` > class, for removal in 4.0; > * Deprecation of ``GiftiMetadata`` methods ``get_metadata`` and ``get_rgba``; > ``GiftiDataArray`` methods ``get_metadata``, ``get_labeltable``, > ``set_labeltable``; ``GiftiImage`` methods ``get_meta``, ``set_meta``. All > these deprecated in favor of corresponding properties, for removal in 4.0; > * Deprecation of ``giftiio`` ``read`` and ``write`` functions in favor of > nibabel ``load`` and ``save`` functions, for removal in 4.0; > * Deprecation of ``gifti.data_tag`` function, for removal in 4.0; > * Deprecation of write-access to ``GiftiDataArray.num_dim``, and new error > when trying to set invalid values for ``num_dim``. We will remove > write-access in 4.0; > * Deprecation of ``GiftiDataArray.from_array`` in favor of ``GiftiDataArray`` > constructor, for removal in 4.0; > * Deprecation of ``GiftiDataArray`` ``to_xml_open, to_xml_close`` methods in > favor of ``to_xml`` method, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.Outputter`` class in favor of > ``GiftiImageParser``, for removal in 4.0; > * Deprecation of ``parse_gifti_fast.parse_gifti_file`` function in favor of > ``GiftiImageParser.parse`` method, for removal in 4.0; > * Deprecation of ``loadsave`` functions ``guessed_image_type`` and > ``which_analyze_type``, in favor of new API where each image class tests the > file for compatibility during load, for removal in 4.0; > > NGUNS, on behalf of all Nibabelers, > > Matthew > _______________________________________________ > 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 arokem at gmail.com Thu Aug 25 10:20:00 2016 From: arokem at gmail.com (Ariel Rokem) Date: Thu, 25 Aug 2016 07:20:00 -0700 Subject: [Neuroimaging] Multiprocessing the multivoxel fit In-Reply-To: References: Message-ID: Hi, On Tue, Aug 23, 2016 at 11:26 AM, Ariel Rokem wrote: > Clarification: > > On Mon, Aug 22, 2016 at 4:40 PM, Ariel Rokem wrote: > >> Hi Eleftherios, >> >> On Mon, Aug 22, 2016 at 2:27 PM, Eleftherios Garyfallidis < >> garyfallidis at gmail.com> wrote: >> >>> I want to attend but the proposed time is not good can you suggest an >>> alternative time or setup a doodle? >>> >> >> OK -- here is a poll with a few times that week: http://whenisgood.net/3w >> m744k >> > > All times are PST. > > Looks like maybe Thursday at 11 AM PST might work (only Eleftherios responded to the poll). I moved the hangout to that time, and let me know if that does not work for you. Cheers, Ariel > Cheers, > > Ariel > > > >> >> >> >>> On Mon, Aug 22, 2016, 2:45 PM Ariel Rokem wrote: >>> >>>> Hi everyone, >>>> >>>> Shahnawaz, soon to be a Google Summer of Code alumnus, expressed >>>> interest in working on multiprocessing the multivoxel fits in dipy (along >>>> the lines of this issue: https://github.com/nipy/dipy/issues/1026). >>>> This would be a good time to revisit that issue and make comments if you >>>> have any. We've also scheduled a hang-out to discuss this: next Monday >>>> (August 29th), at 11 AM PST. If you are interested in joining the >>>> conversation, please let me know, so that I can add you to that hang-out. >>>> >>>> Cheers, >>>> >>>> Ariel >>>> _______________________________________________ >>>> 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 avesani at fbk.eu Thu Aug 25 13:14:19 2016 From: avesani at fbk.eu (Paolo Avesani) Date: Thu, 25 Aug 2016 19:14:19 +0200 Subject: [Neuroimaging] Summer School on Brain Connectomics 19-22 September 2016 Message-ID: *SUMMER SCHOOL ON BRAIN CONNECTOMICS**SEPT. 19-22, DEPT. OF COMPUTER SCIENCE, UNIVERSITY OF VERONA* Connectomics is one of the hottest inter-disciplinary topics today. It links computer science and Engineering with life sciences and medicine. Connection networks grow over functional (fMRI, ASL, EEG) and structural (diffusion weighted MRI) data and the integration of the two in both static and dynamic conditions would shad light on the way our brain actually works. Connectomics also holds paramount potential for clinical applications through the characterization of the network modulation in pathologies and the assessment of the effectiveness of the treatment. The School on Brain Connectomics gathers the knowledge in the different fields that are touched by this topics providing the students a comprehensive view of this research area as well as awareness about the cutting-edge methodological, experimental and clinical aspects that are involved, besides giving them the opportunity of getting in touch with top-level scientists. The School articulates in four days respectively focusing on diffusion MRI and microstructure (Session 1), functional neuroimaging (Session 2), connectivity models (Session 3) and practical aspects (Session 4), complemented by ?Diving Into Science? (DIS) sessions. The School will be held at the Dept. of Computer Science of the University of Verona. The opening lecture will be held by Prof. *Rachid Deriche*, winner of the ERC Advanced grant with the project CoBCoM ?Computational Brain Connectivity Mapping?. Full program is available on the website at www.brainconnectomics.org. *LIST OF SPEAKERS* *Jean Philippe Thiran*, Signal Processing Lab. (LTS5), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland *Maxime Descoteaux*, Sherbrook Connectivity Imaging Lab. (SCIL), Dept. Of Computer Science, Sherbrook University, Canada *Flavio Dell?Acqua*, Centre for Neuroimaging Sciences, King?s College London, UK *Alessandro Daducci*, Radiology Dept., Vaud University Hospital (CHUV) and LTS5-EPFL, Switzerland *Markus Nilsson*, Department of Radiology at Lund University, Sweden *Dimitri Vandeville*, EPFL and University of Geneva, Switzerland *Luis Lemieux*, Department of Clinical and Experimental Epilepsy, UCL, UK *Olivier Coulon*, MeCA research group ? Laboratory for Signals and Systems (LSIS), CNRS, Marseille, France *Angelo Bifone*, Center for Neuroscience and Cognitive Systems, IIT, Italy *Fabio Babiloni*, Univ. La Sapienza and BrainSigns, Rome, Italy *Dr. Cristina Granziera*, Harvard Medical School, US, and CHUV, Lausanne, Switzerland The school will be open to about 50 qualified, motivated and pre-selected candidates. Ph. D. students, Post-Docs, young researchers (both academic and industrial), senior researchers (both academic and industrial) or academic/industrial professionals are encouraged to apply by sending an email to info at brainconnectomics.org. Priority will be given to PhD students. The School fee will be 150,00 ?. Applications should be received *before Sept. 2, 2016*. Applicants will receive notification of acceptance by Sept. 9, 2016. *STUDENT POSTERS AND BEST PRESENTATION* Students may submit a poster to present their research activity. The electronic version of the posters will also be available from the School web site. A best presentation prize of 100? will be assigned by the school committee. *DIS (DIVING INTO SCIENCE) SESSIONS* Groups of students will be formed leaded by a tutor for each topic. The tutor will select 2 papers per each speaker of the Session to be read by the students in the topic group. The DIS session will consist in an open discussion chaired by the tutor with the speakers of the topic. *SCHOOL DEADLINES* Application: *Sept. 2 2016* Notification Acceptance: *Sept. 9 2016* Poster Submission: *Sept. 2 2016* Local Arrangements: available under request on a first-come first-served basis -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbpoline at gmail.com Thu Aug 25 13:41:08 2016 From: jbpoline at gmail.com (JB Poline) Date: Thu, 25 Aug 2016 10:41:08 -0700 Subject: [Neuroimaging] Summer School on Brain Connectomics 19-22 September 2016 In-Reply-To: References: Message-ID: Hi Paolo, Funny and may be a bit sad that this conflict with the brain connectivity conference and brainhack in Vienna ! cheers JB On 25 August 2016 at 10:14, Paolo Avesani wrote: > *SUMMER SCHOOL ON BRAIN CONNECTOMICS**SEPT. 19-22, DEPT. OF COMPUTER > SCIENCE, UNIVERSITY OF VERONA* > > Connectomics is one of the hottest inter-disciplinary topics today. It > links computer science and Engineering with life sciences and medicine. > Connection networks grow over functional (fMRI, ASL, EEG) and structural > (diffusion weighted MRI) data and the integration of the two in both static > and dynamic conditions would shad light on the way our brain actually > works. Connectomics also holds paramount potential for clinical > applications through the characterization of the network modulation in > pathologies and the assessment of the effectiveness of the treatment. > > The School on Brain Connectomics gathers the knowledge in the different > fields that are touched by this topics providing the students a > comprehensive view of this research area as well as awareness about the > cutting-edge methodological, experimental and clinical aspects that are > involved, besides giving them the opportunity of getting in touch with > top-level scientists. > > The School articulates in four days respectively focusing on diffusion MRI > and microstructure (Session 1), functional neuroimaging (Session 2), > connectivity models (Session 3) and practical aspects (Session 4), > complemented by ?Diving Into Science? (DIS) sessions. > > The School will be held at the Dept. of Computer Science of the University > of Verona. > > The opening lecture will be held by Prof. *Rachid Deriche*, winner of the > ERC Advanced grant with the project CoBCoM ?Computational Brain > Connectivity Mapping?. > > Full program is available on the website at www.brainconnectomics.org. > *LIST OF SPEAKERS* > > *Jean Philippe Thiran*, Signal Processing Lab. (LTS5), Swiss Federal > Institute of Technology (EPFL), Lausanne, Switzerland > > *Maxime Descoteaux*, Sherbrook Connectivity Imaging Lab. (SCIL), Dept. Of > Computer Science, Sherbrook University, Canada > > *Flavio Dell?Acqua*, Centre for Neuroimaging Sciences, King?s College > London, UK > > *Alessandro Daducci*, Radiology Dept., Vaud University Hospital (CHUV) > and LTS5-EPFL, Switzerland > > *Markus Nilsson*, Department of Radiology at Lund University, Sweden > > *Dimitri Vandeville*, EPFL and University of Geneva, Switzerland > > *Luis Lemieux*, Department of Clinical and Experimental Epilepsy, UCL, UK > > *Olivier Coulon*, MeCA research group ? Laboratory for Signals and > Systems (LSIS), CNRS, Marseille, France > > *Angelo Bifone*, Center for Neuroscience and Cognitive Systems, IIT, Italy > > *Fabio Babiloni*, Univ. La Sapienza and BrainSigns, Rome, Italy > > *Dr. Cristina Granziera*, Harvard Medical School, US, and CHUV, Lausanne, > Switzerland > > The school will be open to about 50 qualified, motivated and pre-selected > candidates. > > Ph. D. students, Post-Docs, young researchers (both academic and > industrial), senior researchers (both academic and industrial) or > academic/industrial professionals are encouraged to apply by sending an > email to info at brainconnectomics.org. Priority will be given to PhD > students. > > The School fee will be 150,00 ?. > > Applications should be received *before Sept. 2, 2016*. Applicants will > receive notification of acceptance by Sept. 9, 2016. > > > *STUDENT POSTERS AND BEST PRESENTATION* > > Students may submit a poster to present their research activity. The > electronic version of the posters will also be available from the School > web site. > > A best presentation prize of 100? will be assigned by the school committee. > > > *DIS (DIVING INTO SCIENCE) SESSIONS* > > Groups of students will be formed leaded by a tutor for each topic. The > tutor will select 2 papers per each speaker of the Session to be read by > the students in the topic group. The DIS session will consist in an open > discussion chaired by the tutor with the speakers of the topic. > > > *SCHOOL DEADLINES* > > Application: *Sept. 2 2016* > Notification Acceptance: *Sept. 9 2016* > Poster Submission: *Sept. 2 2016* > > > Local Arrangements: available under request on a first-come first-served > basis > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From albayenes at gmail.com Fri Aug 26 10:17:46 2016 From: albayenes at gmail.com (=?UTF-8?B?RW5lcyBBbGJheSAtINin2YbYsyDYp9mE2KjYp9mJ?=) Date: Fri, 26 Aug 2016 17:17:46 +0300 Subject: [Neuroimaging] Saving and reusing ODF Message-ID: Hi everyone, You know that computing ODF takes long time so, I want to save computed odf and reuse after it. What is the best way doing this in dipy? Is there any special way or can I use pickle for saving odf? -- Enes Albay -------------- next part -------------- An HTML attachment was scrubbed... URL: From keschenb at uw.edu Fri Aug 26 17:51:16 2016 From: keschenb at uw.edu (Kristian M. Eschenburg) Date: Fri, 26 Aug 2016 14:51:16 -0700 Subject: [Neuroimaging] Tracking from surface files Message-ID: Hello I'm interested in tracking streamlines using a mesh like that included in the HCP files, instead voxels, as seed points. Does Dipy have this functionality? Thanks! k -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Fri Aug 26 19:19:35 2016 From: arokem at gmail.com (Ariel Rokem) Date: Fri, 26 Aug 2016 18:19:35 -0500 Subject: [Neuroimaging] Tracking from surface files In-Reply-To: References: Message-ID: Hi Kristian, On Fri, Aug 26, 2016 at 4:51 PM, Kristian M. Eschenburg wrote: > Hello > > I'm interested in tracking streamlines using a mesh like that included in > the HCP files, instead voxels, as seed points. Does Dipy have this > functionality? > Thanks for your email. Seeds in dipy (e.g., inputs to the `LocalTracking` class ` __init__` function; see example: https://github.com/nipy/dipy/blob/master/doc/examples/introduction_to_basic_tracking.py#L98 ) are an array of 3D coordinates, so they don't have to be voxels. But - I don't think we don't have a utility function that does what `seeds_from_mask` does, but for meshes (a seeds_from_mesh function). Do the mesh files from HCP contain the 3D positions of the vertices? You could potentially use the positions of the vertices as seeds. A more sophisticated approach would sample the surface of the mesh between vertices. But I haven't thought about this very deeply, and I'd be curious to hear if others have thought about potential pitfalls with these approaches. If you end up writing something along these lines (even just sampling the vertices) consider contributing that alongside seeds_from_mask! Cheers, Ariel > Thanks! > > > k > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arokem at gmail.com Fri Aug 26 19:22:22 2016 From: arokem at gmail.com (Ariel Rokem) Date: Fri, 26 Aug 2016 18:22:22 -0500 Subject: [Neuroimaging] Saving and reusing ODF In-Reply-To: References: Message-ID: Hi Enes, On Fri, Aug 26, 2016 at 9:17 AM, Enes Albay - ??? ????? wrote: > Hi everyone, > > Thanks for writing. > You know that computing ODF takes long time so, I want to save computed > odf and reuse after it. What is the best way doing this in dipy? Is there > any special way or can I use pickle for saving odf? > > The most concise way to save these is using the spherical harmonic coefficients that are used to derive the ODF. Deriving the ODF from these coefficients anew is not nearly as time-consuming as computing these coefficients in the first place. I have been saving these as NiFTI files, because this allows me to save them alongside the spatial transformation of the data (the affine), so that doesn't get lost along the way. Cheers, Ariel > > -- > Enes Albay > > _______________________________________________ > 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 Fri Aug 26 19:45:08 2016 From: garyfallidis at gmail.com (Eleftherios Garyfallidis) Date: Fri, 26 Aug 2016 23:45:08 +0000 Subject: [Neuroimaging] Saving and reusing ODF In-Reply-To: References: Message-ID: Hi Enes, If you want to save the ODFs and then start tracking after we have some code which is still not in dipy/master but please feel free to use it. Here is the link https://github.com/Garyfallidis/dipy/blob/cbrain/dipy/io/peaks.py#L9 Basically, the idea here is that you are saving the peaks object (with the ODFs included if you like) and then you can load it load later for doing tracking etc. Cheers, Eleftherios On Fri, Aug 26, 2016 at 7:23 PM Ariel Rokem wrote: > Hi Enes, > > On Fri, Aug 26, 2016 at 9:17 AM, Enes Albay - ??? ????? < > albayenes at gmail.com> wrote: > >> Hi everyone, >> >> Thanks for writing. > > >> You know that computing ODF takes long time so, I want to save computed >> odf and reuse after it. What is the best way doing this in dipy? Is there >> any special way or can I use pickle for saving odf? >> >> > The most concise way to save these is using the spherical harmonic > coefficients that are used to derive the ODF. Deriving the ODF from these > coefficients anew is not nearly as time-consuming as computing these > coefficients in the first place. I have been saving these as NiFTI files, > because this allows me to save them alongside the spatial transformation of > the data (the affine), so that doesn't get lost along the way. > > Cheers, > > Ariel > > >> >> -- >> Enes Albay >> >> _______________________________________________ >> 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 mrbago at gmail.com Fri Aug 26 21:31:03 2016 From: mrbago at gmail.com (Bago) Date: Sat, 27 Aug 2016 01:31:03 +0000 Subject: [Neuroimaging] Tracking from surface files In-Reply-To: References: Message-ID: Hi all, I believe both of Ariels suggestions are good. Using the mesh vertices as indices should be pretty clean, but sampling points on the mesh will allow you to more finely control the density and number of seeds. I thing worth mentioning is that fiber tracking works best when the seeds are in the white matter tissues, so projecting 1 - 2mm from the mesh into the white matter (when the mesh is along a white/gray boundary) might make the final tacks better. Bago On Fri, Aug 26, 2016 at 4:21 PM Ariel Rokem wrote: > Hi Kristian, > > On Fri, Aug 26, 2016 at 4:51 PM, Kristian M. Eschenburg > wrote: > >> Hello >> >> I'm interested in tracking streamlines using a mesh like that included in >> the HCP files, instead voxels, as seed points. Does Dipy have this >> functionality? >> > > Thanks for your email. > > Seeds in dipy (e.g., inputs to the `LocalTracking` class ` __init__` > function; see example: > https://github.com/nipy/dipy/blob/master/doc/examples/introduction_to_basic_tracking.py#L98 > ) are an array of 3D coordinates, so they don't have to be voxels. But - I > don't think we don't have a utility function that does what > `seeds_from_mask` does, but for meshes (a seeds_from_mesh function). > > Do the mesh files from HCP contain the 3D positions of the vertices? You > could potentially use the positions of the vertices as seeds. A more > sophisticated approach would sample the surface of the mesh between > vertices. But I haven't thought about this very deeply, and I'd be curious > to hear if others have thought about potential pitfalls with these > approaches. If you end up writing something along these lines (even just > sampling the vertices) consider contributing that alongside > seeds_from_mask! > > Cheers, > > Ariel > > >> Thanks! >> >> >> k >> >> _______________________________________________ >> 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 keschenb at uw.edu Fri Aug 26 22:18:18 2016 From: keschenb at uw.edu (Kristian M. Eschenburg) Date: Fri, 26 Aug 2016 19:18:18 -0700 Subject: [Neuroimaging] Tracking from surface files In-Reply-To: References: Message-ID: Hello Thanks for the input, both suggestions are promising ideas. I agree -- projecting the white / gray surface inwards makes sense in order to bypass the weak diffusion signal at the tissue boundary. One could then grow the tracks outwards tangentially to intersect with the actual cortex, or just define cortical labels on this new surface. k On Fri, Aug 26, 2016 at 6:31 PM, Bago wrote: > Hi all, > I believe both of Ariels suggestions are good. Using the mesh vertices > as indices should be pretty clean, but sampling points on the mesh will > allow you to more finely control the density and number of seeds. I thing > worth mentioning is that fiber tracking works best when the seeds are in > the white matter tissues, so projecting 1 - 2mm from the mesh into the > white matter (when the mesh is along a white/gray boundary) might make the > final tacks better. > > Bago > > On Fri, Aug 26, 2016 at 4:21 PM Ariel Rokem wrote: > >> Hi Kristian, >> >> On Fri, Aug 26, 2016 at 4:51 PM, Kristian M. Eschenburg >> wrote: >> >>> Hello >>> >>> I'm interested in tracking streamlines using a mesh like that included >>> in the HCP files, instead voxels, as seed points. Does Dipy have this >>> functionality? >>> >> >> Thanks for your email. >> >> Seeds in dipy (e.g., inputs to the `LocalTracking` class ` __init__` >> function; see example:https://github.com/nipy/dipy/blob/master/doc/ >> examples/introduction_to_basic_tracking.py#L98 ) are an array of 3D >> coordinates, so they don't have to be voxels. But - I don't think we don't >> have a utility function that does what `seeds_from_mask` does, but for >> meshes (a seeds_from_mesh function). >> >> Do the mesh files from HCP contain the 3D positions of the vertices? You >> could potentially use the positions of the vertices as seeds. A more >> sophisticated approach would sample the surface of the mesh between >> vertices. But I haven't thought about this very deeply, and I'd be curious >> to hear if others have thought about potential pitfalls with these >> approaches. If you end up writing something along these lines (even just >> sampling the vertices) consider contributing that alongside >> seeds_from_mask! >> >> Cheers, >> >> Ariel >> >> >>> Thanks! >>> >>> >>> k >>> >>> _______________________________________________ >>> Neuroimaging mailing list >>> Neuroimaging at python.org >>> https://mail.python.org/mailman/listinfo/neuroimaging >>> >>> _______________________________________________ >> Neuroimaging mailing list >> Neuroimaging at python.org >> https://mail.python.org/mailman/listinfo/neuroimaging >> > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From v-nataliam at alleninstitute.org Tue Aug 30 13:05:27 2016 From: v-nataliam at alleninstitute.org (Natalia Mesa) Date: Tue, 30 Aug 2016 17:05:27 +0000 Subject: [Neuroimaging] trouble with fileslice Message-ID: Hi, I'm trying to extract an ROI from a large binary file. Whenever I run nibabel.fileslice.fileslice, I'm getting the following error: C:\Anaconda2\lib\site-packages\nibabel\fileslice.pyc in optimize_read_slicers(sliceobj, in_shape, itemsize, heuristic) 560 if not isinstance(read_slicer, Integral): 561 post_slicers.append(post_slicer) --> 562 stride*=dim_len 563 564 return tuple(read_slicers), tuple(post_slicers) TypeError: unsupported operand type(s) for *=: 'getset_descriptor' and 'int' I'm calling this function with the following: filepath = filepath dtype = 'uint16' chunksize = int((npix*nframes)) sliceobj=slice((0,20,None),(0,20,None)) f = open(filepath, 'r') dat=nibabel.fileslice.fileslice(f, sliceobj=sliceobj, shape=(2048,2048,100), dtype=np.uint16) The binary file I'm trying to analyze is imaging data, and thus the final shape of the array is 3D. The slice object I'm inputting is a 20 by 20 pixel ROI. Thanks! Natalia -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Wed Aug 31 13:20:16 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 31 Aug 2016 10:20:16 -0700 Subject: [Neuroimaging] trouble with fileslice In-Reply-To: References: Message-ID: Hi, On Tue, Aug 30, 2016 at 10:05 AM, Natalia Mesa wrote: > Hi, > > > > I?m trying to extract an ROI from a large binary file. Whenever I run > nibabel.fileslice.fileslice, I?m getting the following error: > > > > > > C:\Anaconda2\lib\site-packages\nibabel\fileslice.pyc in > optimize_read_slicers(sliceobj, in_shape, itemsize, heuristic) > > 560 if not isinstance(read_slicer, Integral): > > 561 post_slicers.append(post_slicer) > > --> 562 stride*=dim_len > > 563 > > 564 return tuple(read_slicers), tuple(post_slicers) > > > > TypeError: unsupported operand type(s) for *=: 'getset_descriptor' and 'int' > > > > I?m calling this function with the following: > > filepath = filepath > > dtype = 'uint16' > > chunksize = int((npix*nframes)) > > > > sliceobj=slice((0,20,None),(0,20,None)) > > > > f = open(filepath, 'r') > > > > dat=nibabel.fileslice.fileslice(f, sliceobj=sliceobj, shape=(2048,2048,100), > dtype=np.uint16) > > > > The binary file I?m trying to analyze is imaging data, and thus the final > shape of the array is 3D. The slice object I?m inputting is a 20 by 20 pixel > ROI. I think you actually want: sliceobj = (slice(0,20,None), slice(0,20,None)) This gives you the equivalent of slicing like `arr[:20, :20]`. I also see that you'll need to do: import numpy as np dtype = np.dtype('uint16') The function could be smarter about working that out, I'll fix that up. Does that work for you? Matthew From matthew.brett at gmail.com Wed Aug 31 13:36:25 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 31 Aug 2016 10:36:25 -0700 Subject: [Neuroimaging] trouble with fileslice In-Reply-To: References: Message-ID: On Wed, Aug 31, 2016 at 10:20 AM, Matthew Brett wrote: > Hi, > > On Tue, Aug 30, 2016 at 10:05 AM, Natalia Mesa > wrote: >> Hi, >> >> >> >> I?m trying to extract an ROI from a large binary file. Whenever I run >> nibabel.fileslice.fileslice, I?m getting the following error: >> >> >> >> >> >> C:\Anaconda2\lib\site-packages\nibabel\fileslice.pyc in >> optimize_read_slicers(sliceobj, in_shape, itemsize, heuristic) >> >> 560 if not isinstance(read_slicer, Integral): >> >> 561 post_slicers.append(post_slicer) >> >> --> 562 stride*=dim_len >> >> 563 >> >> 564 return tuple(read_slicers), tuple(post_slicers) >> >> >> >> TypeError: unsupported operand type(s) for *=: 'getset_descriptor' and 'int' >> >> >> >> I?m calling this function with the following: >> >> filepath = filepath >> >> dtype = 'uint16' >> >> chunksize = int((npix*nframes)) >> >> >> >> sliceobj=slice((0,20,None),(0,20,None)) >> >> >> >> f = open(filepath, 'r') >> >> >> >> dat=nibabel.fileslice.fileslice(f, sliceobj=sliceobj, shape=(2048,2048,100), >> dtype=np.uint16) >> >> >> >> The binary file I?m trying to analyze is imaging data, and thus the final >> shape of the array is 3D. The slice object I?m inputting is a 20 by 20 pixel >> ROI. > > I think you actually want: > > sliceobj = (slice(0,20,None), slice(0,20,None)) > > This gives you the equivalent of slicing like `arr[:20, :20]`. > > I also see that you'll need to do: > > import numpy as np > dtype = np.dtype('uint16') > > The function could be smarter about working that out, I'll fix that up. Here's the fix-up: https://github.com/nipy/nibabel/pull/485 Matthew