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ANTsX / ITKR

port of ITK to R
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Cannot find modules #43

Closed muschellij2 closed 5 years ago

muschellij2 commented 5 years ago

Installed from remotes::install("stnava/ITKR"):

When trying to run ANTsR::kellyKapowski (cort_thickness wraps this) and all files exist, getting error:

> res = cort_thickness("TISSUES.nii.gz", "GM.nii.gz", "WM.nii.gz", verbose = TRUE)
Running DiReCT for 3-dimensional images.

Exception caught: 
itk::ExceptionObject (0x55f61a2d3bf0)
Location: "unknown" 
File: /scratch/temp/125998.1.shared.q/RtmplDdUp6/R.INSTALL6ab21576e92e/ITKR/src/itks/Modules/Core/Common/src/itkProcessObject.cxx
Line: 1412
Description: itk::ERROR: CastImageFilter(0x55f66b597260): Input Primary is required but not set.

Session information

> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                                      
 version  R version 3.6.1 Patched (2019-09-06 r77160)
 os       CentOS Linux 7 (Core)                      
 system   x86_64, linux-gnu                          
 ui       X11                                        
 language (EN)                                       
 collate  en_US.UTF-8                                
 ctype    en_US.UTF-8                                
 tz       US/Eastern                                 
 date     2019-10-04                                 

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version   date       lib source                            
 ANTsRCore   * 0.7.1     2019-09-24 [1] Github (ANTsX/ANTsRCore@0a8a992)  
 assertthat    0.2.1     2019-03-21 [2] CRAN (R 3.6.1)                    
 cli           1.1.0     2019-03-19 [2] CRAN (R 3.6.1)                    
 colorout    * 1.2-2     2019-09-03 [1] Github (jalvesaq/colorout@641ed38)
 crayon        1.3.4     2017-09-16 [2] CRAN (R 3.6.1)                    
 ITKR          0.5.1     2019-10-01 [1] Github (stnava/ITKR@b17d351)      
 lattice       0.20-38   2018-11-04 [3] CRAN (R 3.6.1)                    
 magrittr      1.5       2014-11-22 [2] CRAN (R 3.6.1)                    
 Matrix        1.2-17    2019-03-22 [3] CRAN (R 3.6.1)                    
 Rcpp          1.0.2     2019-07-25 [2] CRAN (R 3.6.1)                    
 RcppEigen     0.3.3.5.0 2018-11-24 [2] CRAN (R 3.6.1)                    
 sessioninfo   1.1.1     2018-11-05 [2] CRAN (R 3.6.1)                    
 withr         2.1.2     2018-03-15 [2] CRAN (R 3.6.1)
muschellij2 commented 5 years ago

FYI - happens locally as well.

stnava commented 5 years ago

ok - this looks very tricky.

when I run the example from ?kellyKapowski, I see the same thing ( in verbose mode ) but the thickness image looks correct.

I saw something similar with antsMotionCorr and massaged some C++ and it disappeared .... but not sure what the issue was.

stnava commented 5 years ago

is the thickness image produced / correct?

stnava commented 5 years ago

I've identified the problem but not the fix just yet

stnava commented 5 years ago

resolved here 554b696927351c0de998fa6cde346c16630212fb

stnava commented 5 years ago

sorry: https://github.com/ANTsX/ANTs/commit/7906d7325453015c886ec13b14f78808e3c43c66 @ntustison @gdevenyi minor bug fix

ntustison commented 5 years ago

Thanks @stnava . Interesting that this as causing problems.

gdevenyi commented 5 years ago

Result of the itk version tag update?

stnava commented 5 years ago

Yes, I think so

On Sun, Oct 6, 2019 at 12:26 PM Gabriel A. Devenyi notifications@github.com wrote:

Result of the itk version tag update?

— You are receiving this because you were mentioned.

Reply to this email directly, view it on GitHub https://github.com/stnava/ITKR/issues/43?email_source=notifications&email_token=AACPE7VK7JQAGDZERRF5GB3QNIGR5A5CNFSM4I5UUGVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAOOA3Y#issuecomment-538763375, or mute the thread https://github.com/notifications/unsubscribe-auth/AACPE7XMU5FN7NL7YSWPR7DQNIGR5ANCNFSM4I5UUGVA .

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brian

muschellij2 commented 5 years ago

Result is there, seems to look OK. Only see the message when verbose = TRUE. Likely not a real issue but a warning that's just showing some issues with linking.

Edit: that is not true - it just returns the GM probability image!

muschellij2 commented 5 years ago

New installation seems to work for me. @stnava - I don't know if you made changes but new installation results in a cortical thickness image.

stnava commented 5 years ago

yes - that was fixed - I don't recall what the issue was - something trivial

brian

On Wed, Oct 23, 2019 at 8:39 AM John Muschelli notifications@github.com wrote:

New installation seems to work for me. @stnava https://github.com/stnava

  • I don't know if you made changes but new installation results in a cortical thickness image.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stnava/ITKR/issues/43?email_source=notifications&email_token=AACPE7QC4XXBLSH5ZC7USILQQBAYJA5CNFSM4I5UUGVKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECBICZY#issuecomment-545423719, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACPE7WTJQKTJGRB3SSF6BTQQBAYJANCNFSM4I5UUGVA .