elastix-imageregistration

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Welcome to the elastix-imageregistration forum! Here you can post questions about open source software for medical image registration, including elastix (http://elastix.isi.uu.nl), SimpleElastix (http://simpleelastix.github.io/), SuperElastix (https://github.com/SuperElastix/SuperElastix), and the Continuous Registration Challenge (https://continuousregistration.grand-challenge.org/).

ANNOUNCEMENT: This group is being replaced by GitHub Discussions: https://github.com/SuperElastix/elastix/discussions, so from now on you can post there! This list will remain open to new replies or posts until 31/03/2023, and it will only act as an archive of past conversations after that date.

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7/14/23

Elastix on MacBook Pro M2 Pro/ M2 Max

Hi, Does the new MacBook Pro M2 Pro and MacBook Pro M2 Max meet the requirements to run elastix

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Elastix on MacBook Pro M2 Pro/ M2 Max

Hi, Does the new MacBook Pro M2 Pro and MacBook Pro M2 Max meet the requirements to run elastix

7/14/23

Mohammad Javad Shojaei

4/24/23

Request for Assistance with Saving Results in Floating Point Format

Hello everyone, I performed rigid registration with just rotation and translation. However, when

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Request for Assistance with Saving Results in Floating Point Format

Hello everyone, I performed rigid registration with just rotation and translation. However, when

4/24/23

Mohammad Javad Shojaei

4/5/23

Inquiry about negative mutual information values in image registration

Hello everyone, I have a question regarding the reported mutual information that is negative. In a

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Inquiry about negative mutual information values in image registration

Hello everyone, I have a question regarding the reported mutual information that is negative. In a

4/5/23

Konstantinos Ntatsis

4/4/23

Elastix presentation and demos, April & May 2023!

Dear community, We are planning some online elastix presentations and demos in April and May. The

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Elastix presentation and demos, April & May 2023!

Dear community, We are planning some online elastix presentations and demos in April and May. The

4/4/23

Kunal Yadav, Konstantinos Ntatsis2

4/4/23

Elastix5.1.0 C++ project failure at elastix translation example

Hi Kunal, We are transitioning to github discussions: https://github.com/SuperElastix/elastix/

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Elastix5.1.0 C++ project failure at elastix translation example

Hi Kunal, We are transitioning to github discussions: https://github.com/SuperElastix/elastix/

4/4/23

Rose, … mfk165

4/3/23

Specify name for output file in elastix/transformix

Hi Rose, What MATLAB wrapper are you using? I use a matlab wrapper and it's possible to change

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Specify name for output file in elastix/transformix

Hi Rose, What MATLAB wrapper are you using? I use a matlab wrapper and it's possible to change

4/3/23

Konstantinos Ntatsis2

4/3/23

ANNOUNCEMENT: Moving to GitHub Discussusions

Hello everyone, In order to use Github Discussions in the same way that you were using this email

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ANNOUNCEMENT: Moving to GitHub Discussusions

Hello everyone, In order to use Github Discussions in the same way that you were using this email

4/3/23

Kunal Yadav, Niels Dekker7

3/23/23

Building ElastiX source code for 32-bit binary for C++ project

Hi Niels, I did tried executing the sample example code "ElastixTranslationExample.cxx",

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Building ElastiX source code for 32-bit binary for C++ project

Hi Niels, I did tried executing the sample example code "ElastixTranslationExample.cxx",

3/23/23

Mohammad Javad Shojaei, N. Heath Patterson4

3/17/23

Request for Advice on Image Registration Issue

Dear Heath, Many thanks for your advice. I followed it, but unfortunately, I still have the same

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Request for Advice on Image Registration Issue

Dear Heath, Many thanks for your advice. I followed it, but unfortunately, I still have the same

3/17/23

2/18/23

Internal working/Cost function minimization or implementation of Mask thing while Registration

KINDLY SOMEONE HELP PLEASE On Sunday, 12 February, 2023 at 7:45:25 pm UTC+5:30 Anmol Namdev wrote:

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Internal working/Cost function minimization or implementation of Mask thing while Registration

KINDLY SOMEONE HELP PLEASE On Sunday, 12 February, 2023 at 7:45:25 pm UTC+5:30 Anmol Namdev wrote:

2/18/23

1/16/23

elastix 5.1.0 released!

Dear all, I'm very pleased to announce that we have just released elastix 5.1.0! elastix 5.1.0 is

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elastix 5.1.0 released!

Dear all, I'm very pleased to announce that we have just released elastix 5.1.0! elastix 5.1.0 is

1/16/23

1/10/23

Super simple question about fixed/moving/transformix

Hello everyone Many people reading this will know the answer to this immediately. I wonder if I have

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Super simple question about fixed/moving/transformix

Hello everyone Many people reading this will know the answer to this immediately. I wonder if I have

1/10/23

Anmol Namdev, mfk166

1/9/23

URGENT: Issue in using Transform Rigidity Penalty Metric

I believe I got something to work - but your mask wasn't good and it was causing the registration

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URGENT: Issue in using Transform Rigidity Penalty Metric

I believe I got something to work - but your mask wasn't good and it was causing the registration

1/9/23

1/4/23

Final voxel size

Hi, I'm new to using Elastix, but have been successful using a MATLAB wrapper I've found (

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Final voxel size

Hi, I'm new to using Elastix, but have been successful using a MATLAB wrapper I've found (

1/4/23

Onder Nazim Onak

12/30/22

Failed to write image in to the file

I have been getting the following ITK error when I try to write the Result image into the file Error:

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Failed to write image in to the file

I have been getting the following ITK error when I try to write the Result image into the file Error:

12/30/22

Mohammad Javad Shojaei2

12/16/22

Error: Bounding box of the mask lies entirely out of the Input Image Region!

Hello everyone, I fixed it. Those masks were generated by VGG, but I generated them again with FIJI,

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Error: Bounding box of the mask lies entirely out of the Input Image Region!

Hello everyone, I fixed it. Those masks were generated by VGG, but I generated them again with FIJI,

12/16/22

Mohammad Javad Shojaei, Niels Dekker5

12/13/22

Issue with registration- Get a registered black image

Dear Niels, Many thanks. I chose both HE and TIC as the fix image, and did registration, but both

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Issue with registration- Get a registered black image

Dear Niels, Many thanks. I chose both HE and TIC as the fix image, and did registration, but both

12/13/22

11/18/22

Registration of 4D BOLD MRI data

Hi all, I wonder if elastix supports the registration of 4D BOLD MRI data and if anyone can provide

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Registration of 4D BOLD MRI data

Hi all, I wonder if elastix supports the registration of 4D BOLD MRI data and if anyone can provide

11/18/22

11/18/22

Registration of 4D BOLD MRI data

Hi all, I wonder if elastix supports the registration of 4D BOLD MRI data and if anyone can provide

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Registration of 4D BOLD MRI data

Hi all, I wonder if elastix supports the registration of 4D BOLD MRI data and if anyone can provide

11/18/22

10/31/22

Registration of brain T1W pre and post contrast

Hi, I have 3D T1W volumes before and after contrast which I would like to register. There is a sort

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Registration of brain T1W pre and post contrast

Hi, I have 3D T1W volumes before and after contrast which I would like to register. There is a sort

10/31/22

gaura...@gmail.com

10/31/22

Partial MR scan registration with whole body CT scan

Hello, I am a newcomer in the field of Medical image analysis. I am currently working on CT scan

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Partial MR scan registration with whole body CT scan

Hello, I am a newcomer in the field of Medical image analysis. I am currently working on CT scan

10/31/22

DONATO SARDELLA, Shane Kirkbride3

10/19/22

Elastix on fluorescence microscopy data

Apologies for the delay, I must have failed to hit the send button and then closed the tab with my

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Elastix on fluorescence microscopy data

Apologies for the delay, I must have failed to hit the send button and then closed the tab with my

10/19/22

10/5/22

Hello everyone, Anyone here had experience in registering MRI images using elastix, say, from DCE (

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Hello everyone, Anyone here had experience in registering MRI images using elastix, say, from DCE (

10/5/22

Ivana Mihalek, … Soren Christensen7

10/1/22

ok, thank you! On Saturday, October 1, 2022 at 11:55:49 AM UTC+2 sor...@gmail.com wrote: I believe

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ok, thank you! On Saturday, October 1, 2022 at 11:55:49 AM UTC+2 sor...@gmail.com wrote: I believe

10/1/22

9/29/22

Registration of brain images with elastix

Hi everyone, I have the following brain images for each patient: T1, T1 post contrast, T2W, and FLAIR

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Registration of brain images with elastix

Hi everyone, I have the following brain images for each patient: T1, T1 post contrast, T2W, and FLAIR

9/29/22

9/1/22

Default branch elastix git repository renamed from "develop" to "main"

For your information, We have just renamed the default (main) branch of https://github.com/

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Default branch elastix git repository renamed from "develop" to "main"

For your information, We have just renamed the default (main) branch of https://github.com/

9/1/22

8/22/22

4D registration enquiry

Hi, I have 4D CT dataset that is basically lots of DCM files (DICOM), each group of DCMs present a 3D

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4D registration enquiry

Hi, I have 4D CT dataset that is basically lots of DCM files (DICOM), each group of DCMs present a 3D

8/22/22

Patrik Brynolfsson, m.st...@lumc.nl2

8/15/22

Generalize a 2D BSplines transform to 3D

Dear Patrick, Three comments come to mind: - the parameters are ordered as follows: first all x

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Generalize a 2D BSplines transform to 3D

Dear Patrick, Three comments come to mind: - the parameters are ordered as follows: first all x

8/15/22

4/12/22

Domain of rigid mask in Rigidity Penalty

Hello all, I have a question regarding the rigidity penalty described in the paper: M. Staring, S.

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Domain of rigid mask in Rigidity Penalty

Hello all, I have a question regarding the rigidity penalty described in the paper: M. Staring, S.

4/12/22

Martin Zukovec, … v.o.van_...@lumc.nl4

3/15/22

SimpleElastix - current state of development

Hi Chitresh, This is a draft PR of the merging efforts. https://github.com/SimpleITK/SimpleITK/pull/

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SimpleElastix - current state of development

Hi Chitresh, This is a draft PR of the merging efforts. https://github.com/SimpleITK/SimpleITK/pull/

3/15/22

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