ERROR: UndefVarError: read_annot not defined

[aalfi]

I am new to Julia. I don't understand the problem.

[dfsp-spirit]

It is hard to tell what is going on without seeing your source code.

But my guess is that you did not (install and) load the neuroformats package before calling the read_annot function from the package.

If you did not install it yet, see the installation section on the repo website.

Once installed, load it first with:

using NeuroFormats

All usage examples in the API documentation assume that the package is installed and loaded.

[aalfi]

Thank you, Dr. Schäfer! NeuroFormats is really impressive work!

I did install the package, I am not sure what I have to correct. Plz refer to the code below and let me know if I have to change anything

(@v1.7) pkg> add NeuroFormats [ Info: Use ./NeuroFormats to add or develop the local directory at ~/NeuroFormats. Updating registry at ~/.julia/registries/General.toml Resolving package versions... No Changes to ~/.julia/environments/v1.7/Project.toml No Changes to ~/.julia/environments/v1.7/Manifest.toml

julia> using NeuroFormats

julia> using GLMakie

julia> fs_subject_dir = "/home/alfin/NeuroFormats.jl/test/brain.mgz" "/home/alfin/NeuroFormats.jl/test/brain.mgz"

julia> surf = read_surf(fs_subject_dir, "/home/alfin/NeuroFormats.jl/test/lh.white") ERROR: UndefVarError: read_surf not defined Stacktrace: [1] top-level scope @ REPL[11]:1

[dfsp-spirit]

I cannot reproduce the problem.

I just downloaded Julia 1.7.2, started a fresh session, and everything works as expected. Here are the commands I type, step by step, including Julia installation

First download Julia 1.7.2 (currently the latest version from the official Julia website), then from my system shell, I unpack and start Julia (my OS is 64 bit Linux, so the file I downloaded is called julia-1.7.2-linux-x86_64.tar.gz):

cd ~/Downloads/
tar xzf julia-1.7.2-linux-x86_64.tar.gz
cd julia-1.7.2/
./bin/julia

Then in the julia prompt, install packages:

using Pkg
Pkg.add("NeuroFormats")
Pkg.add("GLMakie")

takes a while and installs stuff. Then run the example:

using NeuroFormats
using GLMakie

mgh = read_mgh(joinpath(tdd(), "subjects_dir/subject1/mri/brain.mgz"))
volume = dropdims(mgh.data, dims = 4) # drop time dimension, we only have one frame here.

axis = range(0, stop = 1, length = size(volume, 1))
scene3d = contour(axis, axis, axis, volume, alpha = 0.1, levels = 6)

Takes a while to precompile the GLMakie package and dependencies, then shows the brain image from the website.

Could you try that? What OS are you on? Or did you download a checkout of the development repo and try to run from that, maybe? Can you install and use functions from any other package?

[aalfi]

I worked on LINUX. The result of the cortical thickness showed up! It appears that I am having a problem connecting my GUI to the server. Everything is fine with the package! Thank you for your assistance!

[dfsp-spirit]

Great to hear that!

And good luck with getting the visualization to show up on the server.

[aalfi]

The result was obtained. Thanks a lot!