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

Alexis Roche alexis.roche at gmail.com
Fri Aug 21 18:57:21 CEST 2015


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I am realizing that the following example script is outdated as it still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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--
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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