Min/Max setting in plotting

[rb643]

I noticed I can set min/max values using limit_fun, but it seem that this is overridden by the actual min and max if they are smaller. I'm generating a series of plots and would ideally like them all to be on the same scale and also all symmetric, is there a way to do so? This is my rough code so far (where cc is simply the contrast I'm plotting in this loop and the colormap is a divergent RdBu map generated with colorbrewer):

  coloredmeshes = vis.symmetric.data.on.subject(subjects_dir,  subject_id,
                                              lh_clust, rh_clust, bg='sulc', rglactions=list( "trans_fun"=limit_fun(-4, 4),'no_vis'=T),
                                              makecmap_options = list('colFn'=colmap))
  img = vis.export.from.coloredmeshes(coloredmeshes, 
                                      colorbar_legend=paste0("Surface Area (t) - ", cc, " - s",smoothness), 
                                      output_img=paste0('./Figures/FS_adult/SA_',cc,'_FWMH',smoothness,'.png'))

[dfsp-spirit]

Hi Richard,

I did not try it yet, but if I remember correctly there is a way to do this, mentioned in the docs for vis_group(). It could be that it works for other functions as well. Try adding a range parameter to makecmap_options:

makecmap_options = list('colFn'=colmap, 'range'=c(-4, 4))

If it does not work let me know and I will check why.

[rb643]

Ah yes I did find that guide, but it didn't seem like this was an allowed input for make_cmap...? Or did I miss something

  coloredmeshes = vis.symmetric.data.on.subject(subjects_dir,  subject_id,
                                               lh_clust, rh_clust, bg='sulc', rglactions=list( "trans_fun"=limit_fun(-4, 4),'no_vis'=T),
                                               makecmap_options = list('colFn'=colmap,'range'=c(-5, 5),'symm'=TRUE))
Error in if (data_range[1] < min(x)) { : 
  missing value where TRUE/FALSE needed

[dfsp-spirit]

You're right. I will have a look and see whether I can make that option available to all vis functions.

[dfsp-spirit]

Could you check whether the fix in 6d83f24 solves your issue? All you have to do is install fsbrain from github to get the new version:

devtools::install_github('dfsp-spirit/fsbrain')

[rb643]

Thanks for looking into this so quickly. It appears though that I am still getting the same error message..

[rb643]

> packageVersion("fsbrain")
[1] ‘0.4.1’
> library(fsbrain)
>   coloredmeshes = vis.symmetric.data.on.subject(subjects_dir,  subject_id,
+                                               lh_clust, rh_clust, bg='sulc', rglactions=list( 'no_vis'=T),
+                                               makecmap_options = list('colFn'=colmap,'range'=c(-4, 4),'symm'=TRUE))
Error in if (data_range[1] < min(x)) { : 
  missing value where TRUE/FALSE needed

[dfsp-spirit]

Is this fsaverage data? If so, could you attach it here or, if you'd rather not, send via email to my email (maintainer address)?

[dfsp-spirit]

If it is data computed in R, you can use freesurferformats::write.fs.curv to save it to a file. (1 per hemi)

[rb643]

I'm plotting a sig.mgh result this way for a number of output (at varying smoothness levels for various group). Full code:

library(fsbrain)

#fsbrain::download_optional_data();
subjects_dir = '/Applications/freesurfer/7.1.1/subjects/'
sjl = read.md.subjects.from.fsgd("./Output/FSGD_Adult_Subgroup.fsgd");
subject_id = 'fsaverage';

colmap = colorRampPalette(RColorBrewer::brewer.pal(11, name="RdBu"))

for (ss in c('5','10','15')){
  for (cc in c("Both-Neither")){
  
  tryCatch({
 
  lh_demo_cluster_file = paste0('Output/freesurfer_adult_subgroup_etiv/lh.area.',ss,'.glmdir/',cc,'/sig.mgh')
  rh_demo_cluster_file = paste0('Output/freesurfer_adult_subgroup_etiv/rh.area.',ss,'.glmdir/',cc,'/sig.mgh')
  lh_clust = freesurferformats::read.fs.morph(lh_demo_cluster_file); 
  rh_clust = freesurferformats::read.fs.morph(rh_demo_cluster_file);   

  print((sum(lh_clust)+sum(rh_clust)))
  coloredmeshes = vis.symmetric.data.on.subject(subjects_dir,  subject_id,
                                              lh_clust, rh_clust, bg='sulc', rglactions=list( 'no_vis'=T),
                                              makecmap_options = list('colFn'=colmap,'range'=c(-4, 4)))
  img = vis.export.from.coloredmeshes(coloredmeshes, 
                                      colorbar_legend=paste0("Surface Area (t) - ", cc, " - s",ss), 
                                      output_img=paste0('./Figures/FS_adult/SA_',cc,'_FWMH',ss,'.png'))
  # close all windows
  while (rgl.cur() > 0) { rgl.close() }
  })
  }
}

All these left and right hemisphere sig.mgh files should be in fsaverage, I can email you an example, but I'm looping through a stack of results here and trying individual ones all throw the same error. Did I miss something? I added one example set here.
sig.zip

[dfsp-spirit]

Thanks for the zip, that will do.

[dfsp-spirit]

Hm, I think you you do not have the correct fsbrain version yet, or you did not restart the R interpreter after installing it. I am getting this plot with the following code and your unzipped data in the same directory:

library('fsbrain')

subjects_dir = file.path(find.freesurferhome()$found_at, "subjects")
subject_id = 'fsaverage';
colmap = colorRampPalette(RColorBrewer::brewer.pal(11, name="RdBu"))

lh_clust = freesurferformats::read.fs.morph('./lh_sig.mgh'); 
rh_clust = freesurferformats::read.fs.morph('./rh_sig.mgh');



coloredmeshes = vis.symmetric.data.on.subject(subjects_dir,  subject_id,
                                              lh_clust, rh_clust, bg='sulc', rglactions=list( 'no_vis'=T),
                                              makecmap_options = list('colFn'=colmap,'range'=c(-4, 4)))

output_img = "./plot.png";
img = vis.export.from.coloredmeshes(coloredmeshes, 
                                    colorbar_legend=paste0("Surface Area (t)"), 
                                    output_img=output_img);

[dfsp-spirit]

issue19_fsbrain.zip

Here is a zip with my script, your data and the produced output.

[rb643]

For some reason I just needed to restart my X11 as well, its working now! Thanks for sorting this out so quickly and efficiently!

[dfsp-spirit]

You're welcome!

[wjddyd66]

Thank you very much.

It was the same problem as above, but it has been resolved.

If you currently install it with R install.package, it will be installed as 0.4.1 Version as above, and the above problem will occur.

devtools::install_github('dfsp-spirit/fsbrain')

As I reinstalled and ran it, it ran without any problems.

[dfsp-spirit]

Great! I will release a new version with the fix on CRAN soon, it seems many people need this feature.

[dfsp-spirit]

This fix is part of CRAN release 0.4.2.