![]() ![]() recon-all returned a “Permission Denied” error. My first hiccup: /Applications/FreeSurfer/7.2.0/subjects/ did not have write permissions. And put what you’d like to call your output folder after the -s flag (I called mine “tutorial_output”). Set the last part (*.nii) to match the name of your NIFTI file. However, if you’re working with a new FreeSurfer install (or one on a university computing cluster) and you’ve not run recon-all before, you might have a few hiccups before you get it working.įirst, you’ll want to try running this line: recon-all -all -i /Applications/FreeSurfer/7.2.0/subjects/ sample_brain_vestib_tutorial.nii -s tutorial_outputĮdit the path if needed to match your FreeSurfer install. FreeSurfer will produce cortical surface maps that you can convert into a STL file for 3D printing. This is the main step - asking FreeSurfer to preprocess your T1. Try to run the FreeSurfer recon_all code. My NIFTI file is called “ sample_brain_vestib_tutorial.nii” - so it’s there and should be good to go! 3. To check that the NIFTI file copied properly, I navigated to my FreeSurfer subjects folder and listed its contents: $ cd /Applications/FreeSurfer/7.2.0/subjectsįsaverage4 sample_brain_vestib_tutorial.nii So, I followed the layer fMRI blog advice to paste a copy of the T1 NIFTI file into: /Applications/freesurfer/7.2.0/subjects However, for just running a few brains for 3D printing fun, I didn’t worry too much about optimal file organization. This was only my second time using FreeSurfer, so I’m not sure of the best practices for file organization (e.g., particularly if you wanted to keep a large number of subjects organized into groups, studies, etc.). Place your T1 NIFTI file into a FreeSurfer folder. So, you do not need to run those lines twice (though it won’t hurt if you do). [Note that, (if you’re installing FreeSurfer fresh, like I did), by completing the FreeSurfer set-up steps, you’ve already completed half of layer fMRI’s step #2, which asks you to set the FREESURFER_HOME directory and run the SetUpFreeSurfer.sh script: # ALREADY RUN ABOVE: These echoes worked fine! So, I then moved on to the layer fMRI blog steps. ![]() Running those 3 lines in my terminal completed the FreeSurfer set-up steps! Before proceeding, to check that I exported these variables correctly, I echoed each: $ echo $FREESURFER_HOME MNI_DIR /Applications/FreeSurfer/7.2.0/mni SUBJECTS_DIR /Applications/FreeSurfer/7.2.0/subjects ![]() Setting up environment for FreeSurfer/FS-FAST (and FSL)įREESURFER_HOME /Applications/FreeSurfer/7.2.0įSFAST_HOME /Applications/FreeSurfer/7.2.0/fsfast This resulted in the following output, which matched the expected output on the FreeSurfer set-up page. Source $FREESURFER_HOME/SetUpFreeSurfer.sh export FREESURFER_HOME=/Applications/FreeSurfer/7.2.0Įxport SUBJECTS_DIR=$FREESURFER_HOME/subjects Specifically, I followed the Mac installation and set-up instructions described here.Īfter following the download steps, I opened a Mac terminal window and ran this code to set up my FreeSurfer environment. This was a pretty quick and relatively painless process. In my case, I installed and ran FreeSurfer locally on my MacBook Pro. If you have access to a university’s computing cluster, they might already have FreeSurfer installed - so you might want to check this first. FreeSurfer is open source software for processing and analyzing (human) brain MRI scans. Start with FreeSurfer.įirst, download FreeSurfer, if you don’t already have the program. If you already frequently use FreeSurfer - and maybe have already run recon-all on your T1s - then you can skip to the end of my tutorial, or just check out the layer fMRI blog for the NIFTI to STL file command.įor the novices, let’s get started: 1. This tutorial is intended for folks who are novices in FreeSurfer. I’ll also talk about the companies I’ve tried for 3D printing (as our lab doesn’t have a 3D printer, and my university’s “public” 3D printers have been shut down due to COVID). Here, however, I’ll note the few things I had to do slightly differently from their tutorial to get everything to work. My tutorial is adapted from this one on the layer fMRI blog. My fiance’s 3D-printed brain, a fun birthday present! ![]()
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