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

Tue Sep 1 23:25:20 CEST 2015

Alexis,

Thank you! I will try these out this week and follow up here or on github
as needed.

Ben

On Mon, Aug 31, 2015 at 7:05 AM, Alexis Roche <alexis.roche at gmail.com>
wrote:

> Hi Ben,
>
> Updated examples can be found here:
> https://github.com/nipy/nireg/tree/master/examples
>
> At the moment, you will be able to do functional/anatomical rigid
> registration using nireg (see code sketch above), but it doesn't implement
> nonrigid registration yet, so it's not recommended for whole-brain
> subject-atlas realignment at the moment.
>
>
> # Basic structural / functional rigid registration using nireg
>
> import nibabel as nb
> import nireg as nr
>
> fun = nb.load('some_functional_image.nii')
> anat = nb.load('some_T1w_image.nii')
>
> R = nr.HistogramRegistration(fun, anat)
> T = R.optimize('rigid')
> fun_t = nr.resample(fun, T.inv(), reference=anat)
>
> nb.save(funt_t, 'resampled_functional_image.nii')
> Alexis
>
> On Mon, Aug 24, 2015 at 12:17 AM, Ben Cipollini <bcipolli at ucsd.edu> wrote:
>
>> 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 I am realizing that the following example script is outdated as it still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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>>> >
>>> >
>>> >
>>> >
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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
>>>
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>>
>>
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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
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
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