From vsochat at stanford.edu Sat Jun 27 21:44:14 2015 From: vsochat at stanford.edu (vanessa sochat) Date: Sat, 27 Jun 2015 12:44:14 -0700 Subject: [Neuroimaging] Welcome to... Message-ID: the new list! Looking forward to lots of good discussion :) Best, Vanessa -- Vanessa Villamia Sochat Stanford University (603) 321-0676 -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Sat Jun 27 23:29:22 2015 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 27 Jun 2015 14:29:22 -0700 Subject: [Neuroimaging] Nipy-devel retired, long live neuroimaging Message-ID: Hi, As y'all may have seen, I subscribed y'all to the new list. I've done my best to replicate your chosen options from the old list, but please do check your subscription settings. As if to welcome the new list, the old nipy-devel admin interface is down at the moment, but when it comes back up, I'll disable new subscriptions to nipy-devel and send an auto-response pointing to this list. Echoing Vanessa - looking forward to lots of neuroimaging-listey goodness, Cheers, Matthew From matthew.brett at gmail.com Sun Jun 28 06:47:17 2015 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 27 Jun 2015 21:47:17 -0700 Subject: [Neuroimaging] Nibabel 2.0.1 bugfix release Message-ID: Hi, I just did a 2.0.1 bugfix release for nibabel. Here is the Changelog: * 2.0.1 (Saturday 27 June 2015) Contributions from Ben Cipollini, Chris Markiewicz, Alexandre Gramfort, Clemens Bauer, github user freec84. * Bugfix release with minor new features; * Added ``axis`` parameter to ``concat_images`` (pr/298) (Ben Cipollini); * Fix for unsigned integer data types in ECAT images (pr/302) (MB, test data and issue report from Github user freec84); * Added new ECAT and Freesurfer data files to automated testing; * Fix for Freesurfer labels error on early numpies (pr/307) (Alexandre Gramfort); * Fixes for PAR / REC header parsing (pr/312) (MB, issue reporting and test data by Clemens C. C. Bauer); * Workaround for reading Freesurfer ico7 surface files (pr/315) (Chris Markiewicz); * Changed to github pages for doc hosting; * Changed docs to point to neuroimaging at python.org mailing list. Thanks very much to y'all for your patient work. Any problems - please let us know. Cheers, Matthew From bohn-peter at hotmail.de Sun Jun 28 14:41:41 2015 From: bohn-peter at hotmail.de (Peter Bohn) Date: Sun, 28 Jun 2015 14:41:41 +0200 Subject: [Neuroimaging] help displaying PET data using Pysurfer Message-ID: Dear Sir or Madam, I am quite new to the list and Pysurfer therefore my question might seem a bit trivial. Is there a way to display PET Data that has been processed with SPM using Pysurfer and if so does a manual exist? Thanks a lot for your help! Cheers Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From bertrand.thirion at inria.fr Sun Jun 28 20:24:30 2015 From: bertrand.thirion at inria.fr (bthirion) Date: Sun, 28 Jun 2015 20:24:30 +0200 Subject: [Neuroimaging] help displaying PET data using Pysurfer In-Reply-To: References: Message-ID: <55903BDE.4050705@inria.fr> Dear Peter, My best advice is to try and reproduce the examples provided (https://pysurfer.github.io/examples/index.html) and adpat them to you use case. In particular, I can imagine that displaying PET images is comparable to displaying fMRIs ? This is a better way to learn than reading a manual IMHO. Best, Bertran On 28/06/2015 14:41, Peter Bohn wrote: > > dDear Sir or Madam, > > I am quite new to the list and Pysurfer therefore my question might > seem a bit trivial. Is there a way to display PET Data that has been > processed with SPM using Pysurfer and if so does a manual exist? > > Thanks a lot for your help! > > Cheers > > Peter > > > > _______________________________________________ > Neuroimaging mailing list > Neuroimaging at python.org > https://mail.python.org/mailman/listinfo/neuroimaging -------------- next part -------------- An HTML attachment was scrubbed... URL: From mwaskom at stanford.edu Mon Jun 29 04:07:09 2015 From: mwaskom at stanford.edu (Michael Waskom) Date: Sun, 28 Jun 2015 19:07:09 -0700 Subject: [Neuroimaging] help displaying PET data using Pysurfer In-Reply-To: <55903BDE.4050705@inria.fr> References: <55903BDE.4050705@inria.fr> Message-ID: Hi, In particular, this example is probably most relevant: https://pysurfer.github.io/examples/plot_fmri_activation_volume.html It shows how to visualize an fMRI statistical volume that is in MNI152 space. If you can get your PET image into such space, I imagine it will work. I don't think anyone who works on PySurfer has experience with PET data, so you'll have to figure out much of it yourself, most likely. I would be somewhat worried about the low spatial resolution in PET and the effects that has on the mapping to the surface, but it might work. Best, Michael On Sun, Jun 28, 2015 at 11:24 AM, bthirion wrote: > Dear Peter, > > My best advice is to try and reproduce the examples provided ( > https://pysurfer.github.io/examples/index.html) and adpat them to you use > case. In particular, I can imagine that displaying PET images is comparable > to displaying fMRIs ? This is a better way to learn than reading a manual > IMHO. > Best, > > Bertran > > > On 28/06/2015 14:41, Peter Bohn wrote: > > dDear Sir or Madam, > > > I am quite new to the list and Pysurfer therefore my question might seem a > bit trivial. Is there a way to display PET Data that has been processed > with SPM using Pysurfer and if so does a manual exist? > > Thanks a lot for your help! > > Cheers > > Peter > > > > _______________________________________________ > Neuroimaging mailing listNeuroimaging at python.orghttps://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 lists at onerussian.com Mon Jun 29 16:37:49 2015 From: lists at onerussian.com (Yaroslav Halchenko) Date: Mon, 29 Jun 2015 10:37:49 -0400 Subject: [Neuroimaging] Nibabel 2.0.1 bugfix release In-Reply-To: References: Message-ID: <20150629143749.GO28964@onerussian.com> On Sat, 27 Jun 2015, Matthew Brett wrote: > Hi, > I just did a 2.0.1 bugfix release for nibabel. Congrats and thanks! Now uploaded to neurodebian. Downstream testing (to see if anything gets broken with a new upload) is still running but so far all in clear. Cheers! -- Yaroslav O. Halchenko, Ph.D. http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org Research Scientist, Psychological and Brain Sciences Dept. 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 alexandre.gramfort at telecom-paristech.fr Tue Jun 30 09:55:05 2015 From: alexandre.gramfort at telecom-paristech.fr (Alexandre Gramfort) Date: Tue, 30 Jun 2015 09:55:05 +0200 Subject: [Neuroimaging] [JOB] MNE software research engineer Message-ID: hi, I have an open position as engineer in my research team in Telecom ParisTech / CNRS LTCI in downtown Paris. The position is for two years to work on MNE-Python and should start before the end of the year. The goal is to help us to develop, maintain, document and promote the MNE open source project [1,2]. [1] http://martinos.org/mne/ [2] https://github.com/mne-tools/mne-python In terms of environment, my team working on neuroscience topics consists of 3 PhD students, 1 Post-Doc and myself. Please forward this announcement to potential candidates. Candidates are expected to have: - master or PhD degree - some experience with neuroimaging and ideally MEG and EEG - programming experience in Python and collaborative software development. - background on signal processing Applications should be sent to myself before Sept. 1st. Thanks Best, Alex -- Alexandre Gramfort, PhD Assistant Professor, TSI, Telecom ParisTech, CNRS LTCI 37-39 Rue Dareau, 75014 Paris, France http://alexandre.gramfort.net alexandre.gramfort at telecom-paristech.fr From jrudascas at gmail.com Tue Jun 30 23:20:50 2015 From: jrudascas at gmail.com (Jorge Rudas) Date: Tue, 30 Jun 2015 16:20:50 -0500 Subject: [Neuroimaging] Dipy - Problem creating the fiber trackting of my data Message-ID: > > Dear Dipy Team > > I have data from GE Medical Systems resonator, with 24 directions and only > axial view. > > I using the examples for your documentation, specificaly > http://nipy.org/dipy/examples_built/tracking_eudx_tensor.html#example-tracking-eudx-tensor > . > > But, i get the fiber tracking bad. The data was convert using dcm2nii from > DICOMs. > > Below, you find two link at my images of fiber tracking. > > https://www.dropbox.com/s/lc3wmv2yb1nz7uf/image%20%281%29.png?dl=0 > > https://www.dropbox.com/s/gaguehp73qqgo0h/image%20%282%29.png?dl=0 > > > Any suggestions to improve the fiber tracking with my data? > > *Jorge Rudas* > *National University of Colombia* > > -------------- next part -------------- An HTML attachment was scrubbed... URL: