#CONVERTING VOLUMES TO STL
####1. unzip
gunzip rh.hippoSfLabels-T1.v10.nii.gz ####2. binarize the volume:
fslmaths rh.hippoSfLabels-T1.v10.nii -bin rh.hippo_bin.nii####3. create tessellated surface of binarized volume:
mri_tessellate rh.hippo_bin.nii.gz 1 rh.hippo####4. convert binary surface to stl format:
mris_convert rh.hippo rh.hippo.stl#EXTRACTING A LABELED REGION
####1. create temp file:
cp lh.hippoSfLabels-T1.v10.mgz lh.hippo.3dprint.mgz####2. convert to nifti:
mri_convert lh.hippo.3dprint.mgz lh.hippo.3dprint.nii.gz####3. set threshold range to the label number (210 for granule cell layer of the dentate gyrus) and binarize mask:
fslmaths lh.hippo.3dprint.nii.gz -uthr 210 -thr 210 -bin lh.hippo.gcdg.nii.gz#CLEANING AND REPAIRING MODEL
##Meshlab (free)
####1. Smoothing
Filters > Smoothing, Fairing, and Deformation > Laplacian Smooth
####2. Export Mesh as .stl
##Netfabb Basic (free)
####1. Click the Platform Overview button (cube with blue information "i" sign) or press F5 ####2. If status says "valid mesh" then it's ready to print. If status says "incorrect mesh" then continue ####3. Click the Repair button (red cross) ####4. Click automatic repair at the bottom right ####5. Select Default repair and click Execute ####6. Click Apply Repair and select Remove Old Part ####7. Check the status of the mesh again by pressing F5 or clicking Platform Overview
#PRINTING/CHANGING SETTINGS W/ MAKERBOT
Models with angles >45 degrees need support -- can't print on air. Rafts are platforms the object is printed on that improves adhesion to the build plate.
####1. Open .stl file with Makerbot Desktop software ####2. If object is large with heavy overhangs, set Support Density to 0.20 and select Extra Support. ####3. Export .stl to .x3g file to a 2 gb or smaller SD card