ANTsR port to windows - Githubissues

ANTsX / ANTsR

R interface to the ANTs biomedical image processing library

https://antsx.github.io/ANTsR

Apache License 2.0

127 stars 35 forks source link

ANTsR port to windows #211

Closed 1alebra2 closed 6 years ago

1alebra2 commented 6 years ago

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

muschellij2 commented 6 years ago

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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stnava commented 6 years ago

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli notifications@github.com wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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1alebra2 commented 6 years ago

DEar John,

thanks for the answer.

I do have a working ITKR. I pulled it form the repository (the newest version) and could install it into R. I will it compare to yours, (thank you). I am stuck with building ANTsRCore.dlll. All works fine till the building of the dll (makevars.win in src). Here the linker hangs. Breaking this I get undefined references to various ITK libs. I can produce dll when ITKR seems not to be needed. e.g. atropos.dll and the first 8 ants...cpp also give a reasonable dll (130k), albeit I have not tested their functionality within R. I also can produce ITKR.dll.a and extract functions from there. But no avail. If it depends on a major coding issue inside ITK, I will have to wait......

Best

Alexander

John Muschelli notifications@github.com schrieb am 09.04.2018 um 16:01:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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1alebra2 commented 6 years ago

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli notifications@github.com wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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muschellij2 commented 6 years ago

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 notifications@github.com wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli notifications@github.com wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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dorianps commented 6 years ago

Once upon a time, I compiled ANTs in Windows using Visual Studio. So in principle those compiled tools on which ANTsR relies can be compiled and work properly. But exactly how to do that within R escapes my knowledge.

Would be fantastic to have ANTsR on Windows, though. It would mean that anybody can get all the useful tools of ANTs without the Linux virtualization.

Dorian

On Mon, Apr 9, 2018, 12:10 John Muschelli notifications@github.com wrote:

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 notifications@github.com wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli <notifications@github.com

wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/211, or mute the thread <

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stnava commented 6 years ago

Can you share the link to your Linux Strategy?

On Mon, Apr 9, 2018 at 7:24 PM dorianps notifications@github.com wrote:

Once upon a time, I compiled ANTs in Windows using Visual Studio. So in principle those compiled tools on which ANTsR relies can be compiled and work properly. But exactly how to do that within R escapes my knowledge.

Would be fantastic to have ANTsR on Windows, though. It would mean that anybody can get all the useful tools of ANTs without the Linux virtualization.

Dorian

On Mon, Apr 9, 2018, 12:10 John Muschelli notifications@github.com wrote:

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 notifications@github.com wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli < notifications@github.com

wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/211, or mute the thread <

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dorianps commented 6 years ago

Here: https://github.com/ANTsX/ANTsR/wiki/Installing-ANTsR-in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc) .

Recent Windows updates have eliminated the need for Developer Mode. All the user has to do now is open Microsoft Store and download a linux distro.

Dorian

On Mon, Apr 9, 2018 at 7:29 PM, stnava notifications@github.com wrote:

Can you share the link to your Linux Strategy?

On Mon, Apr 9, 2018 at 7:24 PM dorianps notifications@github.com wrote:

Once upon a time, I compiled ANTs in Windows using Visual Studio. So in principle those compiled tools on which ANTsR relies can be compiled and work properly. But exactly how to do that within R escapes my knowledge.

Would be fantastic to have ANTsR on Windows, though. It would mean that anybody can get all the useful tools of ANTs without the Linux virtualization.

Dorian

On Mon, Apr 9, 2018, 12:10 John Muschelli notifications@github.com wrote:

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 notifications@github.com wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli < notifications@github.com

wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 <notifications@github.com

wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/211, or mute the thread <

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dorianps commented 6 years ago

By the way, @stnava. Required packages 'magic' and 'psych' are not listed in the installation instruction of Readme.md. I installed ANTsR last night following the online instructions and had to install those packages as well. The correct line on Readme.md should be:

mydeps <- c( "Rcpp", "RcppEigen", "tools", "methods", "magrittr", "rsvd", "magic", "psych" )

On Tue, Apr 10, 2018 at 9:32 AM, Dorian Pustina albnet@gmail.com wrote:

Here: https://github.com/ANTsX/ANTsR/wiki/Installing-ANTsR- in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).

Recent Windows updates have eliminated the need for Developer Mode. All the user has to do now is open Microsoft Store and download a linux distro.

Dorian

On Mon, Apr 9, 2018 at 7:29 PM, stnava notifications@github.com wrote:

Can you share the link to your Linux Strategy?

On Mon, Apr 9, 2018 at 7:24 PM dorianps notifications@github.com wrote:

Once upon a time, I compiled ANTs in Windows using Visual Studio. So in principle those compiled tools on which ANTsR relies can be compiled and work properly. But exactly how to do that within R escapes my knowledge.

Would be fantastic to have ANTsR on Windows, though. It would mean that anybody can get all the useful tools of ANTs without the Linux virtualization.

Dorian

On Mon, Apr 9, 2018, 12:10 John Muschelli notifications@github.com wrote:

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 notifications@github.com wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli < notifications@github.com

wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 < notifications@github.com> wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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muschellij2 commented 6 years ago

These should not have to be downloaded independently as they are in Imports section of the DESCRIPTION file.

The installer should simply be: devtools::install_github("ANTsX/ANTsR")

John

On Tue, Apr 10, 2018 at 9:40 AM, dorianps notifications@github.com wrote:

By the way, @stnava. Required packages 'magic' and 'psych' are not listed in the installation instruction of Readme.md. I installed ANTsR last night following the online instructions and had to install those packages as well. The correct line on Readme.md should be:

mydeps <- c( "Rcpp", "RcppEigen", "tools", "methods", "magrittr", "rsvd", "magic", "psych" )

On Tue, Apr 10, 2018 at 9:32 AM, Dorian Pustina albnet@gmail.com wrote:

Here: https://github.com/ANTsX/ANTsR/wiki/Installing-ANTsR- in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).

Recent Windows updates have eliminated the need for Developer Mode. All the user has to do now is open Microsoft Store and download a linux distro.

Dorian

On Mon, Apr 9, 2018 at 7:29 PM, stnava notifications@github.com wrote:

Can you share the link to your Linux Strategy?

On Mon, Apr 9, 2018 at 7:24 PM dorianps notifications@github.com wrote:

Once upon a time, I compiled ANTs in Windows using Visual Studio. So in principle those compiled tools on which ANTsR relies can be compiled and work properly. But exactly how to do that within R escapes my knowledge.

Would be fantastic to have ANTsR on Windows, though. It would mean that anybody can get all the useful tools of ANTs without the Linux virtualization.

Dorian

On Mon, Apr 9, 2018, 12:10 John Muschelli notifications@github.com wrote:

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 notifications@github.com wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli < notifications@github.com

wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 < notifications@github.com> wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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dorianps commented 6 years ago

When using devtools, probably there is no need to install any dependency manually. But I am using command line installation:

mydeps <- c( "Rcpp", "RcppEigen", "tools", "methods", "magrittr", "rsvd" )
install.packages( pkgs = mydeps, dependencies = TRUE )
$ git clone https://github.com/stnava/ITKR.git
$ git clone https://github.com/ANTsX/ANTsRCore.git
$ git clone https://github.com/ANTsX/ANTsR.git
$ R CMD INSTALL ITKR
$ R CMD INSTALL ANTsRCore
$ R CMD INSTALL ANTsR

On Tue, Apr 10, 2018 at 9:55 AM, John Muschelli notifications@github.com wrote:

These should not have to be downloaded independently as they are in Imports section of the DESCRIPTION file.

The installer should simply be: devtools::install_github("ANTsX/ANTsR")

John

On Tue, Apr 10, 2018 at 9:40 AM, dorianps notifications@github.com wrote:

By the way, @stnava. Required packages 'magic' and 'psych' are not listed in the installation instruction of Readme.md. I installed ANTsR last night following the online instructions and had to install those packages as well. The correct line on Readme.md should be:

mydeps <- c( "Rcpp", "RcppEigen", "tools", "methods", "magrittr", "rsvd", "magic", "psych" )

On Tue, Apr 10, 2018 at 9:32 AM, Dorian Pustina albnet@gmail.com wrote:

Here: https://github.com/ANTsX/ANTsR/wiki/Installing-ANTsR- in-Windows-10-(along-with-FSL,-Rstudio,-Freesurfer,-etc).

Recent Windows updates have eliminated the need for Developer Mode. All the user has to do now is open Microsoft Store and download a linux distro.

Dorian

On Mon, Apr 9, 2018 at 7:29 PM, stnava notifications@github.com wrote:

Can you share the link to your Linux Strategy?

On Mon, Apr 9, 2018 at 7:24 PM dorianps notifications@github.com wrote:

Once upon a time, I compiled ANTs in Windows using Visual Studio. So in principle those compiled tools on which ANTsR relies can be compiled and work properly. But exactly how to do that within R escapes my knowledge.

Would be fantastic to have ANTsR on Windows, though. It would mean that anybody can get all the useful tools of ANTs without the Linux virtualization.

Dorian

On Mon, Apr 9, 2018, 12:10 John Muschelli <notifications@github.com

wrote:

My repo is the same as the one on stnava, just my fork of it for development purposes.

I have tried (at length) but can’t get the linker to go through for Windows

On Mon, Apr 9, 2018 at 10:48 AM 1alebra2 < notifications@github.com> wrote:

Thanks a lot. I will check this. I know about the alternatives on windows (Bash, docker etc), but I was fond of doing it for windows, because a lot of our software is running there. We also have a working Linux version running of all your software on a linux machine

thanks for the hint

A.

stnava notifications@github.com schrieb am 09.04.2018 um 16:13:

Yes . Alternative : @dorianps uses Linux within windows and posted about this on a wiki somewhere

On Mon, Apr 9, 2018 at 10:01 AM John Muschelli < notifications@github.com

wrote:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 < notifications@github.com> wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards A. Brawanski

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1alebra2 commented 6 years ago

Hello

When building the DLL for ANTsRCore I get the following error:

antsrTransform.o:antsrTransform.cpp:(.text$_ZN3itk31BSplineDecompositionImageFilterINS_5ImageIjLj4EEENS1_IdLj4EEEED1Ev[_ZN3itk31BSplineDecompositionImageFilterINS_5ImageIjLj4EEENS1_IdLj4EEEED1Ev]+0x8): undefined reference to `vtable for itk::BSplineDecompositionImageFilter<itk::Image<unsigned int, 4u>, itk::Image<double, 4u> >'

antsrTransform.o:antsrTransform.cpp:(.text$_ZN3itk19ResampleImageFilterINS_5ImageIjLj4EEES2_ddED1Ev[_ZN3itk19ResampleImageFilterINS_5ImageIjLj4EEES2_ddED1Ev]+0x8): undefined reference to `vtable for itk::ResampleImageFilter<itk::Image<unsigned int, 4u>, itk::Image<unsigned int, 4u>, double, double>'

THis happens only for antsrTransfor.o when the linking takes place. Otherwise no other linking complaints. I use the usual setting Rtools.exe etc for Windows.

I think that is not a coding issue (?). Is it depending on the sequence of the linked libs? IN makevars.win libants and libtik are called twice in a row, with Linux 3 or 4 times if I remember right.

Any suggestions are appreciated

John Muschelli notifications@github.com schrieb am 09.04.2018 um 16:01:

This is a major effort.

ITKR should work for Windows currently:

devtools::install_github("muschellij2/ITKR")

But ANTsRCore and ANTsR have not been ported.

John

On Mon, Apr 9, 2018 at 9:51 AM, 1alebra2 notifications@github.com wrote:

Hello all I was trying to port ANTsR to Windows and ended up with ITK not creating reasonable Windows DLLs. The internet says this depends on internal issues in ITK (Defs of general classes in ITK, which cannot be exported, or so). Thus this is an overall design issue of ITK, which to change would be a very major effort? An answer would be appreciated Best regards

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1alebra2 commented 6 years ago

The windows port is finally up and running. Don't ask me how I did this :) I do some testing now in my spare time and keep you posted

dorianps commented 6 years ago

This is great. Can you post how can we do the build?

On Thu, Jul 5, 2018, 12:03 PM 1alebra2 notifications@github.com wrote:

Closed #211 https://github.com/ANTsX/ANTsR/issues/211.

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1alebra2 commented 6 years ago

Thanks for your interest. I want to do some tests yet. I will let you know

Am 05.07.2018 um 18:19 schrieb dorianps notifications@github.com:

This is great. Can you post how can we do the build?

On Thu, Jul 5, 2018, 12:03 PM 1alebra2 notifications@github.com wrote:

Closed #211 https://github.com/ANTsX/ANTsR/issues/211.

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stnava commented 6 years ago

i think interest would be relatively high from at least a few different parties. thanks for this effort!

1alebra2 commented 6 years ago

Hello sorry for the delay in answering you. I tested the windows port. "Antsandarboles" example goes through. Also AntsR seems to work reasonably. I tested some of the introductory examples of the net. Of course I did not test everything. Thus caveat emptor. I did not make any changes to the code, except "rearranging" some of the code and adding some r code to get the "rearranged" code running in R. I would like to detail what I did (including the sources), because I do not have the means to keep coming changes up to date. I would recommend to do this separately. A few caveats: Antapplytransforms.exe of AntS does not work reasonably in my new compilation (with Mingw). ITK throws an error due to itkTransformFactoryBase_h. It runs into "refuse to register". I have no idea at the moment how to change this. I use your "older" windows port of this, which works. Some parameter combinations in the r-based examples throw an "na.rm error". Other combinations work fine. In imathinterface.cpp of antscore is a possible bug: Option GE defines iMathMERadius (line 898),, shouldn't this be iMathGERadius?

I will all what I have put in my dropbox for you to copy. It's only the binaries. Then you can put it a place you like for download. One could simply copy them into the respective directories (Ants bin and the R libraries). Again, everything without guarantee.

Best A.

stnava notifications@github.com schrieb am 06.07.2018 um 13:29: i think interest would be relatively high from at least a few different parties. thanks for this effort! — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub ( https://github.com/ANTsX/ANTsR/issues/211#issuecomment-403007516) , or mute the thread ( https://github.com/notifications/unsubscribe-auth/AkcmUO_BdjwMNolDXzW6cgVQAdqvv2O0ks5uD0oWgaJpZM4TMk-L) .

dorianps commented 6 years ago

With the rapid changes in ANTsR, the most useful would be to have the instructions how to compile ANTsR from scratch, more so than the binaries itself.

Fyi, the ANTs binaries for Windows, I compiled them a while back using Visual Studio.

Dorian

On Tue, Jul 17, 2018 at 2:42 PM 1alebra2 notifications@github.com wrote:

Hello sorry for the delay in answering you. I tested the windows port. "Antsandarboles" example goes through. Also AntsR seems to work reasonably. I tested some of the introductory examples of the net. Of course I did not test everything. Thus caveat emptor. I did not make any changes to the code, except "rearranging" some of the code and adding some r code to get the "rearranged" code running in R. I would like to detail what I did (including the sources), because I do not have the means to keep coming changes up to date. I would recommend to do this separately. A few caveats: Antapplytransforms.exe of AntS does not work reasonably in my new compilation (with Mingw). ITK throws an error due to itkTransformFactoryBase_h. It runs into "refuse to register". I have no idea at the moment how to change this. I use your "older" windows port of this, which works. Some parameter combinations in the r-based examples throw an "na.rm error". Other combinations work fine. In imathinterface.cpp of antscore is a possible bug: Option GE defines iMathMERadius (line 898),, shouldn't this be iMathGERadius?

I will all what I have put in my dropbox for you to copy. It's only the binaries. Then you can put it a place you like for download. One could simply copy them into the respective directories (Ants bin and the R libraries). Again, everything without guarantee.

Best A.

stnava notifications@github.com schrieb am 06.07.2018 um 13:29: i think interest would be relatively high from at least a few different parties. thanks for this effort! — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub ( https://github.com/ANTsX/ANTsR/issues/211#issuecomment-403007516) , or mute the thread (

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1alebra2 commented 6 years ago

No problem to give you the sources. The reason why I haven't posted them until now is that the automatic build isn't yet going through. If you can help, it's fine with me Alexander

dorianps notifications@github.com schrieb am 17.07.2018 um 21:16: With the rapid changes in ANTsR, the most useful would be to have the instructions how to compile ANTsR from scratch, more so than the binaries itself. Fyi, the ANTs binaries for Windows, I compiled them a while back using Visual Studio. Dorian On Tue, Jul 17, 2018 at 2:42 PM 1alebra2 notifications@github.com wrote: Hello sorry for the delay in answering you. I tested the windows port. "Antsandarboles" example goes through. Also AntsR seems to work reasonably. I tested some of the introductory examples of the net. Of course I did not test everything. Thus caveat emptor. I did not make any changes to the code, except "rearranging" some of the code and adding some r code to get the "rearranged" code running in R. I would like to detail what I did (including the sources), because I do not have the means to keep coming changes up to date. I would recommend to do this separately. A few caveats: Antapplytransforms.exe of AntS does not work reasonably in my new compilation (with Mingw). ITK throws an error due to itkTransformFactoryBase_h. It runs into "refuse to register". I have no idea at the moment how to change this. I use your "older" windows port of this, which works. Some parameter combinations in the r-based examples throw an "na.rm error". Other combinations work fine. In imathinterface.cpp of antscore is a possible bug: Option GE defines iMathMERadius (line 898),, shouldn't this be iMathGERadius?

I will all what I have put in my dropbox for you to copy. It's only the binaries. Then you can put it a place you like for download. One could simply copy them into the respective directories (Ants bin and the R libraries). Again, everything without guarantee.

Best A.

stnava notifications@github.com schrieb am 06.07.2018 um 13:29: i think interest would be relatively high from at least a few different parties. thanks for this effort! — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub ( https://github.com/ANTsX/ANTsR/issues/211#issuecomment-403007516) , or mute the thread (

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muschellij2 commented 6 years ago

I think it'd be good to know:

1) Are you using ITKR installation or native ITK installation. 2) What have you "rearranged"? How have you done this? What indicated what should be rearranged? 3) Have you compiled ANTsRCore for Windows as well? 4) Can you point us to your repo with the code to see diffs over time?

1alebra2 commented 6 years ago

hello if there is further interest from your side write to me personally (alexander.brawanski@ukr.de)

John Muschelli notifications@github.com schrieb am 19.07.2018 um 20:56: I think it'd be good to know:

Are you using ITKR installation or native ITK installation.

What have you "rearranged"? How have you done this? What indicated what should be rearranged?

Have you compiled ANTsRCore for Windows as well?

Can you point us to your repo with the code to see diffs over time? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub ( https://github.com/ANTsX/ANTsR/issues/211#issuecomment-406379739) , or mute the thread ( https://github.com/notifications/unsubscribe-auth/AkcmUIgTW1W08F6FVR01jHD9WMqfxiZDks5uINZxgaJpZM4TMk-L) .

dorianps commented 6 years ago

Hi @1alebra2

Did this result in a working package on your end. Can you share the instructions for installing ANTsR in Windows?

I am sure it would be of interest to many researchers, and perhaps the crowd can help troubleshoot potential issues of the Windows installation.

1alebra2 commented 6 years ago

Hi we are working on it. I will keep you posted

dorianps notifications@github.com schrieb am 31.07.2018 um 20:58:

Hi @1alebra2 Did this result in a working package on your end. Can you share the instructions for installing ANTsR in Windows? I am sure it would be of interest to many researchers, and perhaps the crowd can help troubleshoot potential issues of the Windows installation. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

muschellij2 commented 6 years ago

I'm testing this out at https://github.com/muschellij2/ANTsRCore/tree/windows, but I'm still not able to get around the problem at https://ci.appveyor.com/project/muschellij2/antsrcore/build/1.0.530#L2217:

Not searching for unused variables given on the command line.
CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.11/Modules/CMakeMinGWFindMake.cmake:12 (message):
  sh.exe was found in your PATH, here:
  C:/Rtools/bin/sh.exe
  For MinGW make to work correctly sh.exe must NOT be in your path.
  Run cmake from a shell that does not have sh.exe in your PATH.
  If you want to use a UNIX shell, then use MSYS Makefiles.
Call Stack (most recent call first):
  CMakeLists.txt:75 (project)

Is it possible to pass -DCMAKE_SH=OFF to the ANTs super build? I thought I did with the cmake in configure.win, but I'm unsure if that goes for all the "making" going on

muschellij2 commented 6 years ago

Is https://github.com/muschellij2/ANTs/blob/fda06f591d9711470a472cbab1c3321520b88b91/SuperBuild.cmake#L199 the correct way?

1alebra2 commented 6 years ago

I had this problem as well. Usually when you simply restart the command line again after this in the same shell it worked as far as I remember. It is recommended to turn the shell off in CMAKE, you can try, as far as I remember it did not work. Could you do me favor We are stuck with the data for training the random forest model in ants and arboles . We are using Tustison data which are in the net. However, the atropos truth labels given comprise only the four tumor labels with3 others (CSU, white matter, grey matter) missing. So we have only 4 priors for the model which works, but is not as convenient as could be. Any ideas on this. Or would you recommend another approach for tumor segmentation? Best A

Am 10.08.2018 um 16:22 schrieb John Muschelli notifications@github.com:

I'm testing this out at https://github.com/muschellij2/ANTsRCore/tree/windows, but I'm still not able to get around the problem at https://ci.appveyor.com/project/muschellij2/antsrcore/build/1.0.530#L2217:

Not searching for unused variables given on the command line. CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.11/Modules/CMakeMinGWFindMake.cmake:12 (message): sh.exe was found in your PATH, here: C:/Rtools/bin/sh.exe For MinGW make to work correctly sh.exe must NOT be in your path. Run cmake from a shell that does not have sh.exe in your PATH. If you want to use a UNIX shell, then use MSYS Makefiles. Call Stack (most recent call first): CMakeLists.txt:75 (project) Is it possible to pass -DCMAKE_SH=OFF to the ANTs super build?

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stnava commented 6 years ago

Regarding the Tumor Request, I would recommend opening a new issue in the relevant repository

On Fri, Aug 10, 2018 at 1:56 PM 1alebra2 notifications@github.com wrote:

I had this problem as well. Usually when you simply restart the command line again after this in the same shell it worked as far as I remember. It is recommended to turn the shell off in CMAKE, you can try, as far as I remember it did not work. Could you do me favor We are stuck with the data for training the random forest model in ants and arboles . We are using Tustison data which are in the net. However, the atropos truth labels given comprise only the four tumor labels with3 others (CSU, white matter, grey matter) missing. So we have only 4 priors for the model which works, but is not as convenient as could be. Any ideas on this. Or would you recommend another approach for tumor segmentation? Best A

Am 10.08.2018 um 16:22 schrieb John Muschelli <notifications@github.com :

I'm testing this out at https://github.com/muschellij2/ANTsRCore/tree/windows, but I'm still not able to get around the problem at https://ci.appveyor.com/project/muschellij2/antsrcore/build/1.0.530#L2217:

Not searching for unused variables given on the command line. CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.11/Modules/CMakeMinGWFindMake.cmake:12 (message): sh.exe was found in your PATH, here: C:/Rtools/bin/sh.exe For MinGW make to work correctly sh.exe must NOT be in your path. Run cmake from a shell that does not have sh.exe in your PATH. If you want to use a UNIX shell, then use MSYS Makefiles. Call Stack (most recent call first): CMakeLists.txt:75 (project) Is it possible to pass -DCMAKE_SH=OFF to the ANTs super build?

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Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/211#issuecomment-412158700, or mute the thread https://github.com/notifications/unsubscribe-auth/AATyfjCpG_-g_iVsurplYucZzkbVsOkjks5uPclGgaJpZM4TMk-L .

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brian