Registration nii image

[Carmine Pagliaro]

Hi all,
 can anyone tell me how can I register two dicom NiFTi image? i tried with
TrakEM2 but got problem with image import. I would tried with landmark
registration but I don't know how I do.

thk

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Carmine Pagliaro
*Life is for sharing.*

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras-2]

Hello Carmine,

Are those images 3D or 2D?

ignacio

On Fri, Jul 31, 2015 at 3:22 PM, Carmine Pagliaro <[hidden email]
> wrote:

> Hi all,
>  can anyone tell me how can I register two dicom NiFTi image? i tried with
> TrakEM2 but got problem with image import. I would tried with landmark
> registration but I don't know how I do.
>
> thk
>
> --
> Carmine Pagliaro
> *Life is for sharing.*
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

Tel : [phone] - fax : [phone]
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Steffen Vogler]

Hi Carmine,

For the import:
It seem that TrakEM2 uses the general imagej-functionality to open the file. If you do not yet have a NiFti importer installed - try that. However, the NIfTi import plugin (http://rsb.info.nih.gov/ij/plugins/nifti.html) is sometimes a little picky towards the exact meta data format. In this case: Wherever you have your data from try to save it as .mha and use the following importer: http://www.cs.cmu.edu/~kangli/code/MetaImage_Reader_Writer.html
Or load your nifti data into ITK-Snap (http://www.itksnap.org/pmwiki/pmwiki.php) and export it as a mha-file from there. In worst case you would need to find a way to transcribe your data into .tiff so that TrakEM2 can read it.

For the registration:
TrakEM2 is obviously tailored to work with EM-like image content. If you have something like that - you can go ahead. If you have X-ray, CT, MRI-type images you would need to use tools outside the ImageJ-world (I know, it's hard to believe).
To get started with more advanced image registration, I highly recommend 'elastix' (http://elastix.isi.uu.nl). It works as a wrapper program that kind of bundles underlying ITK-functionalities. Due to its clear syntax you do not need to mess around with C++ code but still have all the flexibility at hand (2D, 3D, 4D, multi-model, affine, b-spline etc.).
A good starting point is this small collection of parameter files compiled for different registration tasks: http://elastix.bigr.nl/wiki/index.php/Parameter_file_database

Good luck!
Steffen



On Sunday, August 16, 2015 08:33 CEST, Ignacio Arganda-Carreras <[hidden email]> wrote:

> Hello Carmine,
>
> Are those images 3D or 2D?
>
> ignacio
>
> On Fri, Jul 31, 2015 at 3:22 PM, Carmine Pagliaro <[hidden email]
> > wrote:
>
> > Hi all,
> >  can anyone tell me how can I register two dicom NiFTi image? i tried with
> > TrakEM2 but got problem with image import. I would tried with landmark
> > registration but I don't know how I do.
> >
> > thk
> >
> > --
> > Carmine Pagliaro
> > *Life is for sharing.*
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> Bâtiment 2
> INRA Centre de Versailles-Grignon
> Route de St-Cyr (RD10)
> 78026 Versailles Cedex France
>
> Tel : [phone] - fax : [phone]
> Website: http://sites.google.com/site/iargandacarreras/
> <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html