Transformations not found for the UP DATA when executing DRBUDDI

[cepa995]

Hi,

I am trying to execute DRBUDDI but keep getting the following WARNING:

WARNING!! The transformations were not found for the up data. Is this intentional? DRBUDDI expects DIFFPREP to have been run previously...

How and why is this message produced? Where should I start looking in order to solve this problem - what might be the cause? (I have my ran DIFFPREP previously and I am using _proc.list files from it)

Thanks

[eurotomania]

Okay..

Things have changed A LOT between version3 and version4. There is no DIFFPREP in version4 anymore.

If you use DIFFPREP from version3 then you would have to use the DRBUDDI from version 3 as well.

If you want to use V4, all you have to do is to use the "TORTOISEProcess" or TORTOISEProcess_cuda executables, which do everything. Including the old DIFFPREP, DRBUDDI and so on. Hope this helps.

On Tue, Jan 31, 2023 at 1:40 PM Stefan Milorad Radonjić < @.***> wrote:

Hi,

I am trying to execute DRBUDDI but keep getting the following WARNING:

WARNING!! The transformations were not found for the up data. Is this intentional? DRBUDDI expects DIFFPREP to have been run previously...

How and why is this message produced? Where should I start looking in order to solve this problem - what might be the cause? (I have my ran DIFFPREP previously and I am using _proc.list files from it)

Thanks

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWF2NWTCDPLN67HRQ6DWVFL77ANCNFSM6AAAAAAUMZCIDU . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- M. Okan Irfanoglu Graduate Student & GTA Computer Sciences & Engineering Ohio State University

[cepa995]

Alright, I will try to use V4 instead. Might have more luck with it.

BTW, I did submit request for account access a while ago but did not receive any feedback, and I see that I must be log in in order to download compiled binaries.

Any other way I can get the binaries, or do you suggest I compile it from source instead?

[eurotomania]

The website is in the process of being changed because of an insane amount of spams we are getting. So your application might have been denied among spams by accident.

Just send an email to the address listed on the page and it will be accepted.

ALSO. Only the binaries for V3 are up on the site now. V4 is not 100% finalized and being updated every day so the binaries are not there yet. However, there is a docker version that is up now as well.

So as a summary:

1) If you dont need the new features such as outlier rejection/replacement, slice-to-volume correction, Gibbs ringing correction for partial k-space data and so on you can use the binaries for V3. 2) If you want these features you need V4. Two options for now (it will be 3 in 2-3 weeks). Compile from source or download Docker version. Instructions for both are on github.

Hope this helps.

On Tue, Jan 31, 2023 at 4:23 PM Stefan Milorad Radonjić < @.***> wrote:

Alright, I will try to use V4 instead. Might have more luck with it.

BTW, I did submit request for account access a while ago but did not receive any feedback, and I see that I must be log in in order to download compiled binaries.

Any other way I can get the binaries, or do you suggest I compile it from source instead?

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/2#issuecomment-1411088025, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWBWQKNWMQLJYSRHDKDWVF7FJANCNFSM6AAAAAAUMZCIDU . You are receiving this because you commented.Message ID: @.***>

-- M. Okan Irfanoglu Graduate Student & GTA Computer Sciences & Engineering Ohio State University

[cepa995]

Ah, okay. That makes sense ..

Thanks for the advice! I am currently trying to build TORTOISE V4 from source by following instructions on the page.

Currently facing this issue when CONFIGURING TORTOISE V4:

/usr/bin/c++
/usr/bin/cc
Release
/home/stefan/TORTOISEV4/TORTOISEV4
Boost Found
ITK 530 Release version used!
Eigen found.
/usr/include/eigen3
-- Configuring done
CMake Error at CMakeLists.txt:432 (add_executable):
  Cannot find source file:

    ../src/tools/UnObliqueImage/UnObliqueImage.cxx

CMake Error at CMakeLists.txt:437 (add_executable):
  Cannot find source file:

    ../src/tools/ConvertGEGradientsToBMatrix/ConvertGEGradientsToBMatrix.cxx

CMake Error at CMakeLists.txt:432 (add_executable):
  No SOURCES given to target: UnObliqueImage

CMake Error at CMakeLists.txt:437 (add_executable):
  No SOURCES given to target: ConvertGEGradientsToBMatrix

I will continue debugging tomorrow. It seems to be related to source file location.

If I cannot solve this tomorrow, should I open another issue specific to this problem? Do you think it would be helpful to someone else in the future?

[eurotomania]

Apologies. That was my bad.

I added a couple of new executables recently and had not pushed them yet.

I just did so it should be okay now.

On Tue, Jan 31, 2023 at 5:03 PM Stefan Milorad Radonjić < @.***> wrote:

Ah, okay. That makes sense ..

Thanks for the advice! I am currently trying to build TORTOISE V4 from source by following instructions on the page.

Currently facing this issue when CONFIGURING TORTOISE V4:

/usr/bin/c++ /usr/bin/cc Release /home/stefan/TORTOISEV4/TORTOISEV4 Boost Found ITK 530 Release version used! Eigen found. /usr/include/eigen3 -- Configuring done CMake Error at CMakeLists.txt:432 (add_executable): Cannot find source file:

../src/tools/UnObliqueImage/UnObliqueImage.cxx

CMake Error at CMakeLists.txt:437 (add_executable): Cannot find source file:

../src/tools/ConvertGEGradientsToBMatrix/ConvertGEGradientsToBMatrix.cxx

CMake Error at CMakeLists.txt:432 (add_executable): No SOURCES given to target: UnObliqueImage

CMake Error at CMakeLists.txt:437 (add_executable): No SOURCES given to target: ConvertGEGradientsToBMatrix

I will continue debugging tomorrow. It seems to be related to source file location.

If I cannot solve this tomorrow, should I open another issue specific to this problem? Do you think it would be helpful to someone else in the future?

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/2#issuecomment-1411128488, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWBCVHXRYQFQGCYCM6DWVGD2BANCNFSM6AAAAAAUMZCIDU . You are receiving this because you commented.Message ID: @.***>

-- M. Okan Irfanoglu Graduate Student & GTA Computer Sciences & Engineering Ohio State University

[cepa995]

Thanks, configuration worked!

Although, build fails

/home/stefan/TORTOISEV4/src/tools/EstimateTensor/estimate_tensor_wlls_parser.cxx: In member function ‘void EstimateTensorWLLS_PARSER::InitializeCommandLineOptions()’:
/home/stefan/TORTOISEV4/src/tools/EstimateTensor/estimate_tensor_wlls_parser.cxx:122:48: warning: unknown escape sequence: '\m'
  122 |         std::string description = std::string( "Free water diffusivity in (\mu m)^2/s for N2 fitting. Default: 3000" );
      |                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[  3%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/defines.cxx.o
[  3%] Building CXX object CMakeFiles/DRBUDDI.dir/home/stefan/TORTOISEV4/src/main/DRBUDDI.cxx.o
[  3%] Linking CXX executable /home/stefan/TORTOISEV4/bin/CreateMask
/usr/bin/ld: attempted static link of dynamic object `/usr/lib/x86_64-linux-gnu/libz.so'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/CreateMask.dir/build.make:300: /home/stefan/TORTOISEV4/bin/CreateMask] Error 1
make[1]: *** [CMakeFiles/Makefile2:291: CMakeFiles/CreateMask.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  4%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/tools/RotateBMatrix/rotate_bmatrix.cxx.o
[  4%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/defines.cxx.o
[  4%] Building CXX object CMakeFiles/DRBUDDI.dir/home/stefan/TORTOISEV4/src/main/DRBUDDIBase.cxx.o
[  5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/TORTOISE_global.cxx.o
[  5%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/TORTOISE_global.cxx.o
[  5%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/main/FINALDATA.cxx.o
[  5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineParser.cxx.o
[  5%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineParser.cxx.o
[  5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineOption.cxx.o
[  5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/extract_3Dvolume_from_4D.cxx.o
[  5%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineOption.cxx.o
[  6%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/read_3Dvolume_from_4D.cxx.o
[  7%] Building CXX object CMakeFiles/DRBUDDI.dir/home/stefan/TORTOISEV4/src/main/run_drbuddi_stage.cxx.o
[  7%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/read_bmatrix_file.cxx.o
[  8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/extract_3Dvolume_from_4D.cxx.o
[  8%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/math_utilities.cxx.o
[  8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/read_3Dvolume_from_4D.cxx.o
[  8%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/main/TORTOISE.cxx.o
[  8%] Linking CXX executable /home/stefan/TORTOISEV4/bin/EstimateTensor
/usr/bin/ld: attempted static link of dynamic object `/usr/lib/x86_64-linux-gnu/libz.so'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/EstimateTensor.dir/build.make:459: /home/stefan/TORTOISEV4/bin/EstimateTensor] Error 1
make[1]: *** [CMakeFiles/Makefile2:317: CMakeFiles/EstimateTensor.dir/all] Error 2
[  8%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/main/DIFFPREP.cxx.o
[  8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/read_bmatrix_file.cxx.o
[  8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/math_utilities.cxx.o
[  8%] Linking CXX executable /home/stefan/TORTOISEV4/bin/Vol2SlRegistration
/usr/bin/ld: attempted static link of dynamic object `/usr/lib/x86_64-linux-gnu/libz.so'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/Vol2SlRegistration.dir/build.make:427: /home/stefan/TORTOISEV4/bin/Vol2SlRegistration] Error 1
make[1]: *** [CMakeFiles/Makefile2:239: CMakeFiles/Vol2SlRegistration.dir/all] Error 2

Again, followed instructions from top to bottom, also tried playing with some CMAKE flags which did not do the trick.

Investigating, will report if I find resolution.

[eurotomania]

You will have to do that step in Step3:

sudo apt install zlib1g-dev

https://github.com/eurotomania/TORTOISEV4#3-eigen-installationbefore the compilation. After this it should work.

On Wed, Feb 1, 2023 at 1:51 AM Stefan Milorad Radonjić < @.***> wrote:

Thanks, configuration worked!

Although, build fails

/home/stefan/TORTOISEV4/src/tools/EstimateTensor/estimate_tensor_wlls_parser.cxx: In member function ‘void EstimateTensorWLLS_PARSER::InitializeCommandLineOptions()’:

/home/stefan/TORTOISEV4/src/tools/EstimateTensor/estimate_tensor_wlls_parser.cxx:122:48: warning: unknown escape sequence: '\m'

122 | std::string description = std::string( "Free water diffusivity in (\mu m)^2/s for N2 fitting. Default: 3000" );

  |                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[ 3%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/defines.cxx.o

[ 3%] Building CXX object CMakeFiles/DRBUDDI.dir/home/stefan/TORTOISEV4/src/main/DRBUDDI.cxx.o

[ 3%] Linking CXX executable /home/stefan/TORTOISEV4/bin/CreateMask

/usr/bin/ld: attempted static link of dynamic object `/usr/lib/x86_64-linux-gnu/libz.so'

collect2: error: ld returned 1 exit status

make[2]: *** [CMakeFiles/CreateMask.dir/build.make:300: /home/stefan/TORTOISEV4/bin/CreateMask] Error 1

make[1]: *** [CMakeFiles/Makefile2:291: CMakeFiles/CreateMask.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs....

[ 4%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/tools/RotateBMatrix/rotate_bmatrix.cxx.o

[ 4%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/defines.cxx.o

[ 4%] Building CXX object CMakeFiles/DRBUDDI.dir/home/stefan/TORTOISEV4/src/main/DRBUDDIBase.cxx.o

[ 5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/TORTOISE_global.cxx.o

[ 5%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/TORTOISE_global.cxx.o

[ 5%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/main/FINALDATA.cxx.o

[ 5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineParser.cxx.o

[ 5%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineParser.cxx.o

[ 5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineOption.cxx.o

[ 5%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/extract_3Dvolume_from_4D.cxx.o

[ 5%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/main/antsCommandLineOption.cxx.o

[ 6%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/read_3Dvolume_from_4D.cxx.o

[ 7%] Building CXX object CMakeFiles/DRBUDDI.dir/home/stefan/TORTOISEV4/src/main/run_drbuddi_stage.cxx.o

[ 7%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/read_bmatrix_file.cxx.o

[ 8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/extract_3Dvolume_from_4D.cxx.o

[ 8%] Building CXX object CMakeFiles/EstimateTensor.dir/home/stefan/TORTOISEV4/src/utilities/math_utilities.cxx.o

[ 8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/read_3Dvolume_from_4D.cxx.o

[ 8%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/main/TORTOISE.cxx.o

[ 8%] Linking CXX executable /home/stefan/TORTOISEV4/bin/EstimateTensor

/usr/bin/ld: attempted static link of dynamic object `/usr/lib/x86_64-linux-gnu/libz.so'

collect2: error: ld returned 1 exit status

make[2]: *** [CMakeFiles/EstimateTensor.dir/build.make:459: /home/stefan/TORTOISEV4/bin/EstimateTensor] Error 1

make[1]: *** [CMakeFiles/Makefile2:317: CMakeFiles/EstimateTensor.dir/all] Error 2

[ 8%] Building CXX object CMakeFiles/TORTOISEProcess.dir/home/stefan/TORTOISEV4/src/main/DIFFPREP.cxx.o

[ 8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/read_bmatrix_file.cxx.o

[ 8%] Building CXX object CMakeFiles/Vol2SlRegistration.dir/home/stefan/TORTOISEV4/src/utilities/math_utilities.cxx.o

[ 8%] Linking CXX executable /home/stefan/TORTOISEV4/bin/Vol2SlRegistration

/usr/bin/ld: attempted static link of dynamic object `/usr/lib/x86_64-linux-gnu/libz.so'

collect2: error: ld returned 1 exit status

make[2]: *** [CMakeFiles/Vol2SlRegistration.dir/build.make:427: /home/stefan/TORTOISEV4/bin/Vol2SlRegistration] Error 1

make[1]: *** [CMakeFiles/Makefile2:239: CMakeFiles/Vol2SlRegistration.dir/all] Error 2

Again, followed instructions from top to bottom, also tried playing with some CMAKE flags which did not do the trick.

Investigating, will report if I find resolution.

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/2#issuecomment-1411548475, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWHWVYJCHX2ZNIPR3EDWVIBYRANCNFSM6AAAAAAUMZCIDU . You are receiving this because you commented.Message ID: @.***>

-- M. Okan Irfanoglu Graduate Student & GTA Computer Sciences & Engineering Ohio State University

[cepa995]

Ah, sadly that does not work. I am still looking into it.

I did manage to run it via Docker. However, I would like to be able to debug it. Hopefully I will resolve this by today.

[eurotomania]

Hmm.

Okay.. Let me do a clean compile to see what is going on. I will let you know.

On Wed, Feb 1, 2023 at 2:24 PM Stefan Milorad Radonjić < @.***> wrote:

Ah, sadly that does not work. I am still looking into it.

I did manage to run it via Docker. However, I would like to be able to debug it. Hopefully I will resolve this by today.

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/2#issuecomment-1412598822, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWFX72PEBMN663KD3RTWVKZ7HANCNFSM6AAAAAAUMZCIDU . You are receiving this because you commented.Message ID: @.***>

-- M. Okan Irfanoglu Graduate Student & GTA Computer Sciences & Engineering Ohio State University

[cepa995]

Okay, thanks. So far no luck on my side.

[eurotomania]

Okay it was a version difference between a couple of things. I pushed a new version and updated the readme.

You will have to recompile ITK with the new commands, pull TORTOISE again and recompile it.

Should work.

On Wed, Feb 1, 2023 at 3:27 PM Stefan Milorad Radonjić < @.***> wrote:

Okay, thanks. So far no luck on my side.

— Reply to this email directly, view it on GitHub https://github.com/eurotomania/TORTOISEV4/issues/2#issuecomment-1412679933, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEFQZWH32MQS4IIASZ34DCLWVLBLFANCNFSM6AAAAAAUMZCIDU . You are receiving this because you commented.Message ID: @.***>

-- M. Okan Irfanoglu Graduate Student & GTA Computer Sciences & Engineering Ohio State University

[cepa995]

Ah, perfect. Thanks, it works!