Error in smooth_surf(Temp, 10) :

[jlhanson5]

Hello all,

I got VertexWiseR kickstarted, but have been having trouble importing Freesurfer data using SURFvextract.

Here are the commands I ran:

library(VertexWiseR)
Sys.setenv(FREESURFER_HOME='/Applications/freesurfer/7.4.1/')
system("source /Applications/freesurfer/7.4.1/SetUpFreeSurfer.sh; env", ignore.stdout = TRUE, ignore.stderr = TRUE);
Sys.setenv(PATH = paste(Sys.getenv("PATH"), file.path(Sys.getenv("FREESURFER_HOME"), "bin"), sep = ":"))
Sys.setenv(SUBJECTS_DIR='/Volumes/Project/Hanson/Internal_MRI_Projects/Duke_PAC/Neuroimaging/BIDS/derivatives/Freesurfer_7/')
setwd('/Volumes/Project/Hanson/Internal_MRI_Projects/Duke_PAC/Neuroimaging/BIDS/derivatives/Freesurfer_7/')
Temp<-SURFvextract(sdirpath = "./", 
             filename="./thickness.rds", template="fsaverage6",
             measure="thickness") 
thickness_smoothed = smooth_surf(Temp, 10)

Regardless of what I do with SURFvextract, I can't seem to move that step forward. I stored it as Temp, but also load the thickness.rds file and for both approaches, I get the following errors:

> thickness_smoothed = smooth_surf(Temp, 10)
Checking for VertexWiseR system requirements ... 
Checking for Miniconda or Python environment...
Checking Numpy's version...
Checking for BrainStat package...
Checking BrainStat's analysis data...
No system requirements are missing. ✓ 

Error in smooth_surf(Temp, 10) : 
  surf_data vector should only contain 20484 (fsaverage5), 81924 (fsaverage6) or 14524 (hippocampal vertices) columns

Here's my R sessionInfo

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Ventura 13.7.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] VertexWiseR_1.1.0

loaded via a namespace (and not attached):
 [1] gtable_0.3.6             ggplot2_3.5.1            htmlwidgets_1.6.4        lattice_0.22-6           vctrs_0.6.5              tools_4.4.2              keras_2.15.0             tfruns_1.5.3             doSNOW_1.0.20            bitops_1.0-9             generics_0.1.3           parallel_4.4.2          
[13] tibble_3.2.1             fansi_1.0.6              pkgconfig_2.0.3          R.oo_1.27.0              Matrix_1.7-1             data.table_1.16.2        oro.nifti_0.11.4         RColorBrewer_1.1-3       lifecycle_1.0.4          compiler_4.4.2           stringr_1.5.1            munsell_0.5.1           
[25] RNifti_1.7.0             codetools_0.2-20         snow_0.4-4               htmltools_0.5.8.1        lazyeval_0.2.2           plotly_4.10.4            pillar_1.9.0             whisker_0.4.1            tidyr_1.3.1              R.utils_2.12.3           iterators_1.0.14         abind_1.4-8             
[37] foreach_1.5.2            tidyselect_1.2.1         digest_0.6.37            stringi_1.8.4            dplyr_1.1.4              purrr_1.0.2              splines_4.4.2            fastmap_1.2.0            grid_4.4.2               colorspace_2.1-1         cli_3.6.3                magrittr_2.0.3          
[49] base64enc_0.1-3          utf8_1.2.4               withr_3.0.2              scales_1.3.0             rappdirs_0.3.3           httr_1.4.7               igraph_2.1.1             reticulate_1.39.0        png_0.1-8                R.methodsS3_1.8.2        pkgfilecache_0.1.5       doParallel_1.0.17       
[61] gifti_0.8.0              viridisLite_0.4.2        rlang_1.1.4              Rcpp_1.0.13-1            zeallot_0.1.0            glue_1.8.0               xml2_1.3.6               ciftiTools_0.16.1        freesurferformats_0.1.18 jsonlite_1.8.9           R6_2.5.1                 fs_1.6.5                
[73] tensorflow_2.16.0       
> 

And I'm doing this in R, but got some similar errors in R Studio. Thoughts about troubleshooting this?

Any thoughts are much appreciated! Jamie.

[CogBrainHealthLab]

Hi Jamie, assuming that SURFvextract has completed successfully, Temp would be a list object where Temp[[1]] is the subject list and Temp[[2]] is the thickness data.

You should be able to proceed with smoothing and subsequent analyses with the thickness data within Temp[[2]]. For instance:

thickness_smoothed = smooth_surf(Temp[[2]], 10)

If you don't want the subject list to be combined with the thickness data in a list object, you can optionally set include subj_ID = FALSE, within SURFvextract(), such that the output will be a matrix object containing only the thickness data