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KCL-BMEIS / niftyreg

This project contains command line tools to perform rigid, affine and non-linear registration of nifti or analyse images as well as utilities
BSD 3-Clause "New" or "Revised" License
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Apply transformation to landmark #22

Closed mmodat closed 6 years ago

mmodat commented 6 years ago

In gitlab by @mmodat on Jun 8, 2017, 18:18

For @rsparks Will add an option in reg_transform to apply the transformation to a set of landmarks.

mmodat commented 6 years ago

In gitlab by @mmodat on Jul 25, 2017, 10:26

created branch 22-apply-transformation-to-landmark

mmodat commented 6 years ago

In gitlab by @mmodat on Jul 25, 2017, 12:15

mentioned in commit f1a33be0b0b92d0f6d8a002bcfc79855d7d5b9e2

mmodat commented 6 years ago

In gitlab by @mmodat on Jul 25, 2017, 12:16

@rsparks Could you try this one and let me know if it behaves as you wanted/expected.

mmodat commented 6 years ago

In gitlab by @rsparks on Aug 11, 2017, 17:14

First not sure is this is expected but I am being required to provide a reference image to apply landmark transformations.

Second I get the following error:

C:\EpiNav\build\NiftyReg\install\bin>reg_transform.exe -land C:\Users\rachel.e.sparks\Desktop\RegFD3\outputCPP.nii C:\Users\rachel.e.sparks\Documents\Results\2017_Atlas\elecOutput\AffineLandmarks.txt C:\Users\rachel.e.sparks\Documents\Results\2017_Atlas\elecOutput\NRLandmarks.txt -ref "C:\Users\rachel.e.sparks\Google Drive\average_nonrigid_it_10.nii.gz" [NiftyReg] The specified transformation is a spline parametrisation: [NiftyReg] C:\Users\rachel.e.sparks\Desktop\RegFD3\outputCPP.nii [NiftyReg ERROR] 2 or 3 values are expected per line

Note that this outputCPP.nii is what I get directly from running RegF3D from the CLI tools in this version of NiftyReg.

mmodat commented 6 years ago

In gitlab by @mmodat on Nov 16, 2017, 16:47

Dear Dr Sparks, @rsparks,

Did you ever tried this one after updating the text file that contained the landmark positions?

Yours sincerely, Marc

mmodat commented 6 years ago

In gitlab by @rsparks on Nov 16, 2017, 16:54

Dear Dr. Modat @mmodat,

Thank you I have tried and verified that this one does indeed work, excluding a problem with relative origin information between niftyreg and NifTK. However, this is a transform I assume that I will need to compute.

Yours insincerely,

Rachel

mmodat commented 6 years ago

In gitlab by @mmodat on Nov 16, 2017, 17:24

mentioned in commit 257296d57992a80af2984e371a373f880de3af36

mmodat commented 6 years ago

In gitlab by @mmodat on Nov 16, 2017, 17:27

mentioned in merge request !22

mmodat commented 6 years ago

In gitlab by @mmodat on Nov 16, 2017, 17:29

closed via merge request !22

mmodat commented 6 years ago

In gitlab by @mmodat on Nov 16, 2017, 17:29

closed via commit 6bf84b492050a4b9a93431209babeab9bc8f14da

mmodat commented 6 years ago

In gitlab by @mmodat on Nov 21, 2017, 17:09

mentioned in commit 6bf84b492050a4b9a93431209babeab9bc8f14da