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ANN: DIPY 1.4.1 Released!
by Eleftherios Garyfallidis May 7, 2021

May 7, 2021

Hello all, We are happy to announce two new releases of DIPY: DIPY 1.4.0 and 1.4.1 are out! Please support us by citing DIPY in your papers using the following DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385> DIPY 1.4.1 (Thursday, 6 May 2021) & 1.4.0 (Saturday, 13 March, 2021) - Release 1.4.1 received contributions from 11 developers (the full release notes are at: https://dipy.org/documentation/1.4.1./release_notes/release1.4.1/). - … [View More] Release 1.4.0 received contributions from 8 developers (the full release notes are at: https://dipy.org/documentation/1.4.0./release_notes/release1.4/). Thank you all for your contributions and feedback! Please click here <https://dipy.org/documentation/1.4.1./api_changes/> to check 1.4.1 API changes. Please click here <https://dipy.org/documentation/1.4.0./api_changes/> to check 1.4.0 API changes. Highlights of 1.4.1 release include: - New surface seeding module for tractography named mesh. - Patch2Self and its documentation updated. - BUAN and RecoBundles documentation updated. - Standardization and improvement of the multiprocessing / multithreading rules. - Community and governance information added. - Large update of Cython code in compliance with the last standard. - Large documentation update. - Closed 61 issues and merged 28 pull requests. Highlights of 1.4.0 release include: - New self-supervised denoising algorithm Patch2Self added. - Response function refactored and clarified. - B-tensor allowed with response functions. - Large Command Line Interface (CLI) documentation updated. - Public API for Registration added. - Large documentation update. - Closed 47 issues and merged 19 pull requests. To upgrade or install <http://dipy.org/release0.10.html> DIPY Run the following command in your terminal: <http://dipy.org/release0.10.html> pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (3.0.0+). For visualization you need FURY (0.7.0+). Questions or suggestions? For any questions go to https://dipy.org, or send an e-mail to dipy(a)python.org <neuroimaging(a)python.org> We also have an instant messaging service and chat room available at https://gitter.im/dipy/dipy Finally, a new forum is available at https://github.com/dipy/dipy/discussions Have a wonderful time using the latest release. On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors [View Less]

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DIPY Workshop 2021 starts in a few days - March 15 2021
by Eleftherios Garyfallidis March 9, 2021

March 9, 2021

Hello all, Be happy to register here https://workshop.dipy.org to attend the DIPY workshop. Registration this year is free of charge due to COVID. See attachment for more information. Schedule available at https://workshop.dipy.org [image: image.png] <https://workshop.dipy.org> Best regards, Eleftherios

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ANN: DIPY 1.3.0
by Eleftherios Garyfallidis Nov. 10, 2020

Nov. 10, 2020

Hello all, We are excited to announce a new release of DIPY: DIPY 1.3 is out! Please support us by citing DIPY in your papers using the following DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385> DIPY 1.3.0 (Wednesday, 3 November 2020) This release received contributions from 27 developers (the full release notes are at: https://dipy.org/documentation/1.3.0./release_notes/release1.3/). Thank you all for your contributions and feedback! Please click here &… [View More]

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ANN: DIPY 1.2.0
by Eleftherios Garyfallidis Sept. 17, 2020

Sept. 17, 2020

Hello all, We are excited to announce a new release of DIPY: DIPY 1.2 is out! Please support us by citing DIPY in your papers using the following DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385> DIPY 1.2.0 (Wednesday, 9 September 2020) This release received contributions from 27 developers (the full release notes are at: https://dipy.org/documentation/1.2.0./release_notes/release1.2/). Thank you all for your contributions and feedback! Please click here … [View More]

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ANN: DIPY 1.1.1 - a powerful release
by Eleftherios Garyfallidis Jan. 15, 2020

Jan. 15, 2020

We are excited to announce a new release of DIPY: DIPY 1.1.1 is out! In addition: a) A new 5 day workshop available during March 16-20 to learn the theory and applications of the hundreds of methods available in DIPY 1.1.1 Intense! See the exquisite program here <https://workshop.dipy.org>. *b) Given the need for a myriad of new DIPY derivative projects, DIPY moved to its own organization in GitHub. **Long live DIPY! * *And therefore, *https://github.com/dipy/dipy* supersedes https:/… [View More]/github.com/nipy/dipy <https://github.com/nipy/dipy> The old link will be available as a redirect link for the next 6 months.* c) Please support us by *citing** DIPY* in your papers using the following DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385>otherwise the DIPY citation police will find you. ;) DIPY 1.1.1 (Friday, 10 January 2020) This release received contributions from 11 developers (the full release notes are at: https://dipy.org/documentation/1.1.1./release_notes/release1.1/). Thank you all for your contributions and feedback! Please click here <https://dipy.org/documentation/1.1.1./api_changes/> to check API changes. Highlights of this release include: - New module for deep learning DIPY.NN (uses TensorFlow 2.0). - Improved DKI performance and increased utilities. - Non-linear and RESTORE fits from DTI compatible now with DKI. - Numerical solutions for estimating axial, radial and mean kurtosis. - Added Kurtosis Fractional Anisotropy by Glenn et al. 2015. - Added Mean Kurtosis Tensor by Hansen et al. 2013. - Nibabel minimum version is 3.0.0. - Azure CI added and Appveyor CI removed. - New command line interfaces for LPCA, MPPCA and Gibbs Unringing. - New MTMS CSD tutorial added. - Horizon refactored and updated to support StatefulTractograms. - Speeded up all cython modules by using a smarter configuration setting. - All tutorials updated to API changes and 2 new tutorials added. - Large documentation update. - Closed 126 issues and merged 50 pull requests. Note: - Have in mind that DIPY stopped supporting Python 2 after version 0.16.0. All major Python projects have switched to Python 3. It is time that you switch too. To upgrade or install <http://dipy.org/release0.10.html> DIPY Run the following command in your terminal: <http://dipy.org/release0.10.html> pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (3.0.0+). For visualization you need FURY (0.4.0+). Questions or suggestions? For any questions go to http://dipy.org, or send an e-mail to dipy(a)python.org <neuroimaging(a)python.org> We also have an instant messaging service and chat room available at https://gitter.im/nipy/dipy On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors [View Less]

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Re: confused over rendered results
by Eleftherios Garyfallidis Nov. 6, 2019

Nov. 6, 2019

Yes, you need to enable order_transparency=True in the ShowManager. On Tue, Nov 5, 2019 at 8:07 PM Randy Heiland <randy.heiland(a)gmail.com> wrote: > Do you know if Fury correctly renders translucent polygons? I remember > needing to use one of VTK's polygon depth sorting class years ago. I've > attached a script which seems to render dubious results as you rotate it. > It should be a bunch of semitransparent cyan spheres surrounding opaque red > spheres. > > thanks,… [View More] Randy > > > On Tue, Nov 5, 2019 at 4:30 PM Serge K. <skab12(a)gmail.com> wrote: > >> > I just upgraded fury to 0.4.0 and things seem OK now >> >> Great! >> >> > is it possible to insert some sort of VTK clipping plane into my >> scene? >> >> Yes, but we need to create a function to make it easy. Not so obvious >> right now. >> >> - Serge K. >> >> >> On Tue, Nov 5, 2019 at 4:21 PM Randy Heiland <randy.heiland(a)gmail.com> >> wrote: >> >>> I just upgraded fury to 0.4.0 and things seem OK now. Thanks for being >>> so responsive! I'm sure I'll have more questions later... actually, what >>> about clipping planes - is it possible to insert some sort of VTK clipping >>> plane into my scene? >>> >>> Randy >>> >>> On Tue, Nov 5, 2019 at 4:17 PM Serge K. <skab12(a)gmail.com> wrote: >>> >>>> Can you give us your vtk version too and the result of the command >>>> below? >>>> >>>> python -c "import fury; print(fury.get_info())" >>>> >>>> will try to reproduce it. >>>> >>>> - Serge K. >>>> >>>> On Tue, Nov 5, 2019 at 4:09 PM Randy Heiland <randy.heiland(a)gmail.com> >>>> wrote: >>>> >>>>> Dang. I was afraid that'd be the case. I'm now getting inconsistent >>>>> results - sometimes I see some of the spheres (with radius 5), sometimes >>>>> nothing - attached. >>>>> >>>>> I'm using: >>>>> ~/git/fury_play$ python >>>>> Python 3.6.5 |Anaconda, Inc.| (default, Apr 26 2018, 08:42:37) >>>>> [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin >>>>> >>>>> and: >>>>> In [5]: fury.__version__ >>>>> Out[5]: '0.3.0' >>>>> >>>>> On Tue, Nov 5, 2019 at 3:51 PM Serge K. <skab12(a)gmail.com> wrote: >>>>> >>>>>> Hi Randy, >>>>>> >>>>>> As you can see below, your script works well in my case. So maybe I >>>>>> misunderstood your question or I do not see what is wrong. >>>>>> >>>>>> - Serge K. >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Nov 5, 2019 at 3:43 PM Randy Heiland <randy.heiland(a)gmail.com> >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I've attached a script that I use to render packed spheres. When I >>>>>>> use "box_radius = 3.0", they render as expected. But using "box_radius = >>>>>>> 5.0", I don't see any spheres. Am I misusing the scene rendering commands >>>>>>> at the end? Something else? >>>>>>> >>>>>>> thanks! >>>>>>> Randy >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Fury mailing list -- fury(a)python.org >>>>>>> To unsubscribe send an email to fury-leave(a)python.org >>>>>>> https://mail.python.org/mailman3/lists/fury.python.org/ >>>>>>> >>>>>> [View Less]

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confused over rendered results
by Randy Heiland Nov. 6, 2019

Nov. 6, 2019

Hi, I've attached a script that I use to render packed spheres. When I use "box_radius = 3.0", they render as expected. But using "box_radius = 5.0", I don't see any spheres. Am I misusing the scene rendering commands at the end? Something else? thanks! Randy

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Re: confused over rendered results
by Eleftherios Garyfallidis Nov. 5, 2019

Nov. 5, 2019

I can see them. :) On Tue, Nov 5, 2019 at 3:43 PM Randy Heiland <randy.heiland(a)gmail.com> wrote: > Hi, > > I've attached a script that I use to render packed spheres. When I use > "box_radius = 3.0", they render as expected. But using "box_radius = 5.0", > I don't see any spheres. Am I misusing the scene rendering commands at the > end? Something else? > > thanks! > Randy > >

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ANN: DIPY 1.0.0 - a historic release
by Eleftherios Garyfallidis Aug. 16, 2019

Aug. 16, 2019

We are excited to announce a new major and historic release of Diffusion Imaging in Python (DIPY). DIPY 1.0.0 is out! Please cite using the following DOI: 10.3389/fninf.2014.00008 <https://www.ncbi.nlm.nih.gov/pubmed/24600385> DIPY 1.0.0 (Monday, 5 August 2019) This release received contributions from 17 developers (the full release notes are at: https://dipy.org/documentation/1.0.0./release_notes/release1.0/). Thank you all for your contributions and feedback! A new DIPY era is … [View More]starting: this release is compatible with python 3.5+ and breaks backward compatibility with 0.x.x. Please click here <https://dipy.org/documentation/1.0.0./api_changes/> to check API changes or look at the end of this email. The 0.16.x series will have extended bug-fix-only support for Python 2.7 until June 2020. Highlights of this release include: - Critical API changes <https://dipy.org/documentation/1.0.0./api_changes/> - New awesome website <http://dipy.org> - Large refactoring of tracking API - New denoising algorithm: MP-PCA - New Gibbs ringing removal - New interpolation module: dipy.core.interpolation - New reconstruction models: Mean Signal DKI, MTMS-CSD - Increased coordinate systems consistency - New object to manage safely tractography data: StatefulTractogram - New command line interface for downloading datasets: FetchFlow - Horizon updated, medical visualization interface powered by QuickBundlesX - Removed all deprecated functions and parameters - Removed compatibility with Python 2.7 - Updated minimum dependencies version (Numpy, Scipy) - All tutorials updated to API changes and 3 new added - Large documentation update - Closed 289 issues and merged 98 pull requests Note: - DIPY 0.16.x will be the last series to support python 2. The next release, DIPY 1.0, will support python 3 only. To upgrade or install <http://dipy.org/release0.10.html> DIPY Run the following command in your terminal: <http://dipy.org/release0.10.html> pip install --upgrade dipy or conda install -c conda-forge dipy This version of DIPY depends on nibabel (2.4.0+). For visualization you need FURY (0.3.0+). Questions or suggestions? For any questions go to http://dipy.org, or send an e-mail to dipy(a)python.org <neuroimaging(a)python.org> We also have an instant messaging service and chat room available at https://gitter.im/nipy/dipy On behalf of the DIPY developers, Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro https://dipy.org/contributors API Changes Some of the changes introduced in the 1.0 release will break backwards compatibility with previous versions. This release is compatible with Python 3.5+ Reconstruction The spherical harmonics bases mrtrix and fibernav have been renamed to tournier07 and descoteaux07 after the deprecation cycle started in the 0.15 release. We changed dipy.data.default_sphere from symmetric724 to repulsion724 which is more evenly distributed. Segmentation The API of dipy.segment.mask.median_otsu has changed in the following ways: if you are providing a 4D volume, vol_idx is now a required argument. The order of parameters has also changed. Tractogram loading and saving The API of dipy.io.streamlines.load_tractogram and dipy.io.streamlines.save_tractogram has changed in the following ways: When loading trk, tck, vtk, fib, or dpy) a reference nifti file is needed to guarantee proper spatial transformation handling. Spatial transformation handling Functions from dipy.tracking.streamlines were modified to enforce the affine parameter and uniform docstrings. deform_streamlines select_by_rois, orient_by_rois, _extract_vals and values_from_volume. Functions from dipy.tracking.utils were modified to enforce the affine parameter and uniform docstring. density_map connectivity_matrix, seeds_from_mask, random_seeds_from_mask, target, target_line_based, near_roi, length and path_length were all modified. The function affine_for_trackvis, move_streamlines, flexi_tvis_affine and get_flexi_tvis_affine were deleted. Functions from dipy.tracking.life were modified to enforce the affine parameter and uniform docstring. voxel2streamline, setup and fit from class FiberModel were all modified. afq_profile from dipy.stats.analysis was modified in a similar way. Simulations - dipy.sims.voxel.SingleTensor has been replaced by dipy.sims.voxel.single_tensor - dipy.sims.voxel.MultiTensor has been replaced by dipy.sims.voxel.multi_tensor - dipy.sims.voxel.SticksAndBall has been replaced by dipy.sims.voxel.sticks_and_ball Interpolation All interpolation functions have been moved to a new module name dipy.core.interpolation Tracking The voxel_size parameter has been removed from the following function: - dipy.tracking.utils.connectivity_matrix - dipy.tracking.utils.density_map - dipy.tracking.utils.stremline_mapping - dipy.tracking._util._mapping_to_voxel The dipy.reconst.peak_direction_getter.PeaksAndMetricsDirectionGetter has been renamed dipy.reconst.peak_direction_getter.EuDXDirectionGetter. The LocalTracking and ParticleFilteringTracking functions were moved from dipy.tracking.local.localtrackingto dipy.tracking.local_tracking. They now need to be imported from dipy.tracking.local_tracking. - functions argument tissue_classifier were renamed stopping_criterion The TissueClassifier were renamed StoppingCriterion and moved from dipy.tracking.local.tissue_classifier to dipy.tracking.stopping_criterion. They now need to be imported from dipy.tracking.stopping_criterion. - TissueClassifier -> StoppingCriterion - BinaryTissueClassifier -> BinaryStoppingCriterion - ThresholdTissueClassifier -> ThresholdStoppingCriterion - ConstrainedTissueClassifier -> AnatomicalStoppingCriterion - ActTissueClassifier -> ActStoppingCriterion - CmcTissueClassifier -> CmcStoppingCriterion The dipy.tracking.local.tissue_classifier.TissueClass was renamed dipy.tracking.stopping_criterion.StreamlineStatus. The EuDX tracking function has been removed. EuDX tractography can be performed using dipy.tracking.local_tracking using dipy.reconst.peak_direction_getter.EuDXDirectionGetter. Streamlines dipy.io.trackvis has been removed. Use dipy.io.streamline instead. Other - dipy.external package has been removed. - dipy.fixes package has been removed. - dipy.segment.quickbundes module has been removed. - dipy.reconst.peaks module has been removed. - Compatibility with Python 2.7 has been removed [View Less]

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How to set the scence to show the coronal view of the fiber orientation?
by 卢琪 July 20, 2019

July 20, 2019

Hi, I'm referring to this example Visualize bundles and metrics on bundles to draw the coronal view of the fiber orientation. I want to know if I should use 'window.Scence()'? And how to set the scence to using 'scence.set_camera()' to show the coronal view of the fiber orientation. Yours sincerely, Lu | | 卢琪邮箱：luqily(a)163.com | 签名由网易邮箱大师定制 --------- Forwarded Message --------- From: 卢琪 Date: 07/21/2019 01:03 To: fury-owner Subject: How to set the scence to show the coronal view of … [View More]

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