Data import through import_scn for structural covariance network

[Lei Guo]

Dear Chris,

Thank you very much for developing this great package! I'm starting to use this package to analyze my structural imaging results from Freesurfer. However, I was confused while I using function import_scn. The manual says that subcortical gray matter would also be imported if applicable. But even if I extracted subcortical gray matter volumes from Freesurfer and renamed it to asegstats.csv, the aseg value in imported data was still NULL.  I wonder if I did it wrong. I don't know if I should not import thickness data and subcortical volume simultaneously. 

Here below is my code and data:

raw_data <- import_scn(datadir = '../data/brainGraphData/',

                       atlas = 'dk',modality = 'thickness')

And this is the files in my data directory:

I have checked the data are in the required form because the thickness data were imported successfully. 

 I'm new in this area, and really thanks a lot for your time.

best wishes 

Lei Guo

[Chris Watson]

If you would like to include subcortical volumes, you must select an atlas that includes subcortical regions. In your case, it should probably be 'dk.scgm'.

Chris

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[Lei Guo]

Dear Chris,

Sorry for ignoring this detail. Many thanks for your quick reply. It worked   : ) 

Lei Guo

[Alice Ballerini]

Dear Chris,

I'm using this space because I have the same problem of Lei Guo.

I'm using brainGraph 3.0.2 and R version 4.1.1.

This is my directory:

- aparc_lh_thickness.csv

- aparc_rh_thickness.csv

- asegstats.csv

- covars.csv

When I run 

> raw_data <- import_scn(datadir, atlas='dk', modality='thickness', exclude.subs=exclude.subs)

aseg is NULL

If I replace 'dk' with 'dk.scgm', as you recommended, the output is the following error:

> raw_data <- import_scn(datadir, atlas='dk.scgm', modality='thickness', exclude.subs=exclude.subs)

Error in update_fs_names(asegfile, "aseg", exclude.subs) :

argument "exclude.subs" absent, no default value

What is your advice to fix this error?

Thank you in advance,

Alice

[Chris Watson]

This is actually a bug. You would have to edit the relevant line either in "import.R" or in the function "import_scn". It should be:

scgm <- update_fs_names(asegfile, 'aseg', parc=NULL, hemi=NULL, exclude.subs=exclude.subs)

If you update the R file, you will have to run

source('import.R')

Sorry about this simple bug. I am not sure when I will have time to push an update to GitHub.

Chris

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[Alice Ballerini]

Hi Chris,

I solved the error by modifying the code string in "import.R" file, now it works.

Thank you so much,

have a nice day.

Alice