Issue starting

[tjop92]

I am very unfamiliar with Linux and am trying to figure out how to complete Step 1. I get the zip downloaded and unpacked. But how do I do the following commands? Or is this setting up folders?

Or is it easier using the script? The only problem is that I have no idea how to run that script. Could you help me figure out how to run it?

"Step 1 - Specify Variables

Let's first specify all necessary variables that we need for this to work:

Main folder for the whole project

export EXPERIMENT_DIR=/users/mnotter/3dbrain

Path to the FreeSurfer folder

export SUBJECTS_DIR=$EXPERIMENT_DIR/freesurfer

Name of the subject

export subject=sub001

Path to the structural image

export subjT1=$EXPERIMENT_DIR/${subject}/struct.nii.gz"

[miykael]

@tjop92 - one of the prerequisites for the scripts is the software FreeSurfer, which is only available for Linux or OSX. There are some workarounds for Windows, e.g. using a virtual machine or something called Docker. Once you have everything setup up and are good to go, you need to run a FreeSurfer algorithm, called recon-all for about 8-12h (4h on a powerful machine, using multicores).

If you want to learn how to do this, I'm happy to help you to set everything up. But if you want (and trust me :-)), you can also send me your MRI image and I can create the 3D model for you. Both options are fine for me.

[BynariStar]

I've had good luck running 3Dprinting_brain.sh through WSL on Windows 10, just made a couple changes like sourcing FreeSurfer within the script instead of in .bashrc, and running MeshLab with xvfb due to the lack of a native X server.

It should be pretty simple to create an install script too (not including acquiring a FreeSurfer license). Perhaps that would be useful?

[tjop92]

@miykael What would be a good email address for you? Or I can give you mine. I have the data in a google drive.

Honestly, I want what would be easier for you. I have basically no experience with linux, and am having issues just getting freesurfer installed. So I would imagine that it would take a lot of time and work to get it working on for me. Please let me know what would be best for you. :)

[miykael]

@BynariStar, that's cool. I didn't know about WSL. Does that mean you don't need a dual boot or virtual machine / docker to directly run some linux code on Windows? If you have time and energy, would be a great addition to have such a script as well.

[miykael]

@tjop92 - the best way to reach me is under michaelnotter@hotmail.com. For me, the easiest solution is to create the model for you. So, if you just want your 3D model, no problem, send me your brain.

But if you want to figure out how all of this works, don't hesitate. I'm happy to guide you through linux, FreeSurfer etc.