When calling MRI Preprocessing module with Command YAEL+recon-all, I receive an error about rpyANTs.

[zhangjb35]

Describe the bug
When calling MRI Preprocessing module with Command YAEL+recon-all, I receive an error about rpyANTs.

To Reproduce
Steps to reproduce the behavior:
Please check the scrrenshot.

Screenshots

RAVE Information (please run the following R command):

ravemanager::export_logs()
#> RAVE core package information: 
#>   ravemanager:      1.0.42
#>   rave:             1.0.3.3
#>   ravetools:        0.1.6
#>   filearray:        0.1.6
#>   shidashi:         0.1.6
#>   rpymat:           0.1.7
#>   dipsaus:          0.2.8 [Latest update: 0.2.8.9003]
#>   threeBrain:       1.1.0.9005 [Latest update: 1.1.0.9020]
#>   raveio:           0.9.0.50 [Latest update: 0.9.0.52]
#>   ravedash:         0.1.3.30 [Latest update: 0.1.3.31]
#>   readNSx:          0.0.4
#>   rpyANTs:          0.0.3.9003
#>   rutabaga:         0.1.7
#>   ravebuiltins:     1.0.5
#> ------------------------------
#> * Please update core dependencies using
#> 
#>     lib_path <- Sys.getenv("RAVE_LIB_PATH", unset = Sys.getenv("R_LIBS_USER", unset = .libPaths()[[1]]))
#>     loadNamespace("ravemanager", lib.loc = lib_path)
#>     ravemanager::update_rave()
#> R version 4.3.1 (2023-06-16)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.6 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.utf8         LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Asia/Shanghai
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] styler_1.10.2            sass_0.4.7               xml2_1.3.6              
#>  [4] stringi_1.7.12           digest_0.6.35            magrittr_2.0.3          
#>  [7] evaluate_0.22            fastmap_1.1.1            R.oo_1.25.0             
#> [10] ravedash_0.1.3.30        R.cache_0.16.0           jsonlite_1.8.7          
#> [13] R.utils_2.12.2           dipsaus_0.2.8            backports_1.4.1         
#> [16] formatR_1.14             promises_1.2.0.1         httr_1.4.4              
#> [19] purrr_1.0.2              freesurferformats_0.1.18 jquerylib_0.1.4         
#> [22] cli_3.6.1                shiny_1.7.2              rlang_1.1.1             
#> [25] R.methodsS3_1.8.2        ellipsis_0.3.2           reprex_2.0.2            
#> [28] withr_2.5.1              cachem_1.0.8             yaml_2.3.7              
#> [31] filearray_0.1.6          ravemanager_1.0.42       tools_4.3.1             
#> [34] parallel_4.3.1           checkmate_2.2.0          raveio_0.9.0.50         
#> [37] httpuv_1.6.5             shidashi_0.1.6           png_0.1-8               
#> [40] vctrs_0.6.3              R6_2.5.1                 mime_0.12               
#> [43] lifecycle_1.0.3          stringr_1.5.0            htmlwidgets_1.6.2       
#> [46] fs_1.6.3                 bslib_0.5.1              later_1.3.0             
#> [49] glue_1.6.2               Rcpp_1.0.12              xfun_0.43.7             
#> [52] threeBrain_1.1.0.9005    knitr_1.44               xtable_1.8-4            
#> [55] htmltools_0.5.6.9001     rmarkdown_2.25           shinyWidgets_0.8.5      
#> [58] shinyvalidate_0.1.3      pkgfilecache_0.1.5       compiler_4.3.1          

[dipterix]

Hi @zhangjb35 , you might want to update RAVE (run ravemanager::version_info() and follow the instructions) first. Please remember to close all other R/RStudio sessions before updating, and restart R/RStudio after update for changes to take effect.

Let me know if the issue still exists.

[zhangjb35]

seem nothing change. I use the instructions to update my local installation of RAVE. When I choose to use YALE+Recon all, same error pop up.

[zhangjb35]

I found another error. It is weird. When I call Recon all only , then I run the generated script manually with bash. The recon-all pipeline is done, but the final copy command corrupt.

ri_convert --in_type mgz --out_type nii /home/jinbo/.cache/R/raveio/FreeSurfer/S01/rave-imaging/fs/mri/T1.mgz /home/jinbo/.cache/R/raveio/FreeSurfer/S01/rave-imaging/fs/mri/T1.nii reading from /home/jinbo/.cache/R/raveio/FreeSurfer/S01/rave-imaging/fs/mri/T1.mgz... TR=8.66, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -9.31323e-10, 0) j_ras = (3.72529e-09, 0, -1) k_ras = (-4.65661e-10, 1, 0) writing to /home/jinbo/.cache/R/raveio/FreeSurfer/S01/rave-imaging/fs/mri/T1.nii... cp: cannot create regular file '/home/jinbo/.cache/R/raveio/FreeSurfer/S01/rave-imaging/fs/mri/rave_slices.nii.gz': No such file or directory

When I ls that dir, I got:
ls /home/jinbo/.cache/R/raveio/FreeSurfer/
sub01

[dipterix]

You can ignore that warning. This file only replace the MRI displayed in 3D viewer with the original image rather than FreeSurfer conformed version.

However. This is weird. It seems that you were running on an old version of package raveio as the new version should fix this issue (beauchamplab/raveio#19). Would you mind joining our slack channel (by sending your edu email to [email protected]) so we can schedule a live troubleshooting?