[Neuroimaging] 3d registration for data fusion in material science

[Ben Cipollini]

Alexis,

I'm also interested in having this demo. Is this the right code-path to do
functional/structural alignment within a subject as well as aligning
subject and atlas data?

Thanks,
Ben

On Fri, Aug 21, 2015 at 9:57 AM, Alexis Roche <alexis.roche at gmail.com>
wrote:

> Hi,
>
> I am realizing that the following example script is outdated as it still
> relies on importing nipy:
>
> https://github.com/nipy/nireg/blob/master/examples/affine_registration.py
>
> I will submit an update in a few days. The registration code was
> previously part of the nipy package, which we have recently decided to
> split into several standalone packages, including nireg. The idea is that
> nireg only needs nibabel to run (in addition to the standard numpy/scipy
> packages).
>
>
> > -          how to convert a numpy array to nipy-like image ?
>
> This is done using nibabel, see in particular the Nifti1Image class.
>
> > -          should the two images have the same size ?
>
> No.
>
> > -          the version of nipy that I should use ?
>
> As mentioned above, the latest version of the code does not require nipy.
>
> I will let you know when I push an up-to-date version of the affine
> registration example script.
>
> Best,
>
> Alexis
>
>
> >
> >
> >
> >
> >
> > thank you, really, for your attention, this is kind.
> >
> >
> >
> > Gael
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > De : Neuroimaging [mailto:neuroimaging-bounces+gael.goret=
> cea.fr at python.org] De la part de Alexis Roche
> > Envoyé : vendredi 21 août 2015 13:04
> >
> >
> > À : Neuroimaging analysis in Python
> > Objet : Re: [Neuroimaging] 3d registration for data fusion in material
> science
> >
> >
> >
> > Hi Gael,
> >
> > Beside the stuff in dipy that Elef mentioned, there is another brain
> image registration package that has slowly developed over the years, and
> could be useful to you (although it still crucially lacks documentation):
> >
> > https://github.com/nipy/nireg
> >
> >
> >
> > This is rigid/affine registration only for the time being and has a BSD
> license too.
> >
> >
> >
> > Best,
> >
> > Alexis
> >
> >
> >
> > On Fri, Aug 21, 2015 at 9:57 AM, GORET Gael 246279 <Gael.GORET at cea.fr>
> wrote:
> >
> > Hi all,
> >
> >
> >
> > Thanks for your quick replies,
> >
> > This project is just starting, and there is not too much materials …
> >
> > However, to answer your questions, I just have created a public repo on
> my github account :
> >
> >
> >
> > https://github.com/ggoret/MUDRA
> >
> >
> >
> > -          In /doc, I have placed a summary (a pdf slideshow) of the
> project containing some pictures (and info on instruments)
> >
> >
> >
> > -          In /examples I have put two data volumes (npy binary file
> format) the kind of data I need to register.
> >
> >
> >
> > -          In /mudra a first (naive) try using the Fourier shell
> correlation as metric
> >
> > And you can also find
> >
> > -          a Cython wrapping of malik and perona’s algorithms
> implementation working (pretty quickly) on 3D Volumes :
> >
> > o   /mudra/extensions/non_linear_filtering.pyx
> >
> >
> >
> > -          In /scripts you will find mainly converters simplifying I/O
> >
> > -          In /tools 3 very nice visualization tools based on VTK (not
> mayavi) working as standalone (npy input) :
> >
> > o   elevation.py -> 2d image to 3d landscape
> >
> > o   plan_interpolator.py -> 2d slicing of volume + isosurface rendering
> for given seeds
> >
> > o   scalar_field.py -> volume rendering (color and opacity gradient)
> >
> >
> >
> > Thanks in advance for your advices
> >
> >
> >
> > Cheers,
> >
> >
> >
> > Gael
> >
> >
> >
> > De : Neuroimaging [mailto:neuroimaging-bounces+gael.goret=
> cea.fr at python.org] De la part de Eleftherios Garyfallidis
> > Envoyé : jeudi 20 août 2015 16:35
> > À : Neuroimaging analysis in Python
> > Objet : Re: [Neuroimaging] 3d registration for data fusion in material
> science
> >
> >
> >
> > Hi Gael,
> >
> >
> >
> > Sounds exciting. There is no restriction to use our tools in other
> libraries or domains.
> >
> > Look at these tutorials please (you need dipy development version)
> >
> >
> >
> >
> https://github.com/nipy/dipy/blob/master/doc/examples/affine_registration_3d.py
> >
> >
> https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_2d.py
> >
> >
> https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_3d.py
> >
> >
> >
> > Do you have a github repo of your project? Do you have any example
> pictures/volumes to show us that you would
> >
> > like to register?
> >
> >
> >
> > Cheers,
> >
> > Eleftherios
> >
> >
> >
> >
> >
> >
> >
> > On Thu, Aug 20, 2015 at 9:31 AM, GORET Gael 246279 <Gael.GORET at cea.fr>
> wrote:
> >
> > Hi everybody,
> >
> > I am a (French) newcomer, working on the development of the data fusion
> of Time-of-Flight Secondary Ion Mass Spectrometer (ToF-SIMS) and X ray
> Nano-Tomography (XuM) data at the CEA (the French state institute for
> energy, high-tech, etc.).
> >
> > In terms of samples, we’re a bit far from the neuro-fields … Solid oxide
> fuel cell, 3D chips, Si/Li matrix, etc., but in terms of methodology I hope
> we have to share … my project is to combine a chemical information (from
> ToF-SIMS) with X-ray absorption (given by XuM) for a given volume (at
> nano-scale).  I am tackling a python module aiming to the registration of
> 3d datasets. it seems that nipy includes a such possibility (an a lot more
> …).
> >
> > I’m a computer guy, mostly Pythonist and I wander if you would let  me
> transpose your code (mainly the registration part) to my problematic, I
> would be very grateful for this.
> >
> > In this context would you have some advice for me ?
> >
> > I'm looking forward to hearing from you.
> >
> > Gael
> >
> >
> >
> >
> >
> > Dr. Gaël Goret
> >
> > Chercheur Postdoctoral
> >
> > Département des Technologies Silicium
> >
> > Service de Caractérisation des Matériaux & Composants
> >
> > Commissariat à l’énergie atomique et aux énergies alternatives
> >
> > MINATEC Campus | 17 rue des martyrs | F-38054 Grenoble Cedex
> >
> > T. +33 (0)4 38 78 49 29 | gael.goret at cea.fr
> >
> >
> >
> >
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> >
> >
> >
> > --
> >
> > Lead Clinical Research
> > Advanced Clinical Imaging Technology
> > Siemens/CHUV/EPFL
> > 1015 Lausanne, Switzerland
> > Phone: +41 21 545 9972
> > https://sites.google.com/site/alexisroche
> >
> >
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> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
> >
>
>
>
> --
> Lead Clinical Research
> Advanced Clinical Imaging Technology
> Siemens/CHUV/EPFL
> 1015 Lausanne, Switzerland
> Phone: +41 21 545 9972
> https://sites.google.com/site/alexisroche
>
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