[ITK] Question about applying registration transformation to another data set

[Andras Lasso]

Please post 3D Slicer specific question to the Slicer forum:
https://discourse.slicer.org

Andras

From: Community [mailto:community-bounces at itk.org] On Behalf Of Ivan Hidrovo
Sent: Monday, June 12, 2017 5:45 PM
To: community at itk.org
Subject: Re: [ITK] Question about applying registration transformation to another data set

Hello community,
I know that this is not an itk related question, but does anybody know how to input my own created 0-1 bit mask  for general registration (BRAINS) in 3D slicer?
Thank you,
Ivan

On Mon, Jun 12, 2017 at 2:31 PM, Andras Lasso <lasso at queensu.ca<mailto:lasso at queensu.ca>> wrote:
You must follow my example exactly. Lines are not allowed to be removed or reordered.

Andras

From: Ivan Hidrovo<mailto:ivan.hidrovo at gmail.com>
Sent: Monday, June 12, 2017 3:28 PM
To: Andras Lasso<mailto:lasso at queensu.ca>

Subject: Re: [ITK] Question about applying registration transformation to another data set

Dear Andras,
We tried this :

type: int
dimension: 3
sizes: 91 106 115
endian: little
encoding: raw
data file: m1d0_ROIRegboxS.raw
It loaded nothing (at least not visible in the windows open)
but when we tried a mhd format it appears to show it:

ObjectType = Image
NDims = 3
DimSize = 91 106 115
ElementType = MET_INT
ElementDataFile = m1d0_ROIRegboxS.raw
What are we doing wrong in the nrrd format.
Can we go ahead with mhd ?

On Mon, Jun 12, 2017 at 12:29 PM, Ivan Hidrovo <ivan.hidrovo at gmail.com<mailto:ivan.hidrovo at gmail.com>> wrote:
Dear Andras,
Thank you.
-Ivan

On Mon, Jun 12, 2017 at 12:19 PM, Andras Lasso <lasso at queensu.ca<mailto:lasso at queensu.ca>> wrote:
Yes, you can load raw files into 3D Slicer. You just have to create a small text file that specifies how your raw file should be interpreted (pixel type, image size, spacing). For example, if you have a raw file ‘myimage.raw’ create a text file called ‘myimage.nhdr’ in the same directory with the following content:

NRRD0004
type: short
dimension: 3
space: left-posterior-superior
sizes: 256 256 130
space directions: (1.0,0,0) (0,1.0,0) (0,0,1.0)
kinds: domain domain domain
endian: little
encoding: raw
space origin: (0.0,0.0,0.0)
data file: myimage.raw

Probably you only need to change type (probably uchar, short, or double – see all options here: http://teem.sourceforge.net/nrrd/format.html#basic<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fteem.sourceforge.net%2Fnrrd%2Fformat.html%23basic&data=02%7C01%7Classo%40queensu.ca%7Cf9bded9ae6454207bc0008d4b1c928e2%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636328924909734583&sdata=2WkBPYI0I%2FtaXtqiMxzdBPPtB8W7FoDXM%2B6JfMXBU3w%3D&reserved=0>), sizes (image size in pixels), and space directions (change 1.0 values to image spacing values).

If you create your images in Matlab then you can use nrrdwrite.m to write your matrix into a raw file along with a .nhdr text header file (https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsubversion.assembla.com%2Fsvn%2Fslicerrt%2Ftrunk%2FMatlabBridge%2Fsrc%2FMatlabCommander%2Fcommandserver%2F&data=02%7C01%7Classo%40queensu.ca%7Cf9bded9ae6454207bc0008d4b1c928e2%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636328924909734583&sdata=WWT2Wu4ATC51JBOE7TFoFSx7O9u5USw0qVAYZ6YC1H0%3D&reserved=0>).

You can load the image by drag-and-dropping the .nrrd file into 3DSlicer application window.

Andras

From: Community [mailto:community-bounces at itk.org<mailto:community-bounces at itk.org>] On Behalf Of Ivan Hidrovo
Sent: Monday, June 12, 2017 1:05 PM
To: community at itk.org<mailto:community at itk.org>
Subject: Re: [ITK] Question about applying registration transformation to another data set

Hello community,

Can you kindly tell me
1) if you can input a threshold to an image on ITK when implementing an algorithm?
For example when running registration I wish to use only voxel values within a lower and higher threshold
2) Also,do you know if you can use raw files in Slicer3D? we had difficulty putting raw data into slicer and hence switched to ITK
Thank you,
Ivan

On Fri, Jun 9, 2017 at 12:08 PM, Ivan Hidrovo <ivan.hidrovo at gmail.com<mailto:ivan.hidrovo at gmail.com>> wrote:
Hello all,
We are registering 2 data sets A and B using ImageRegistration8.cxx. We get an output dataset C registered to A and also some matrix numbers which we believe to be the rigid registration parameters.
 We need to apply the same registration transformation to another data set (of a different modality) -- is there a way to use this code or another code to apply a given transformation to an image.
Or do we need to make small changes to the code to do this.
thanks,
Ivan




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