Hi everyone,
I’m trying to represent a fiber tract on a glass brain. I tried several ways but all failed. My fiber tracts are in .tck format. Anyone knows how to generate a figure like the one below? Thanks a lot!
Best,
Chunxiang
2 Likes
You can follow the steps described by Matteo Mancini in Making a glass brain // NeuroSnippets :
- upsample the mask
- use a Gaussian filter to smooth the upsampled mask
- use a threshold to obtain a neat black-and-white result
- dilate the previous volume
- subtract the volume obtained in point 4 from the dilated volume
mrresize mask.mif -scale 5 mask_up.mif
mrfilter mask_up.mif smooth -stdev 2 mask_smooth.mif
mrthreshold mask_smooth.mif -abs 0.5 mask_thres.mif
maskfilter mask_thres.mif dilate -npass 2 mask_dilated.mif
mrcalc mask_dilated.mif mask_thres.mif -subtract glass_brain.mif
Then open glass_brain.mif with mrview and switch to volume renderer view and play with the alpha settings untill you get the desired effect.
9 Likes
@bjeurissen Thank you so much for the detailed response. That really helps.
Best,
Chunxiang
I’m curious @bjeurissen if you can help me with this. I followed those steps exactly. I obtain an image that, when viewed in single slice or ortho mode, has a thin stripe of 1’s but when I turn on volume render there is no brain or outline.
Does the volume renderer work at all? Test this by loading up a normal brain mask or an anatomical scan and then switch to volume rendering. Does it work?
Did you try playing with the intensity scaling, transparency, and alpha? Maybe you have set it up so that the mask is invisible?
Hi @bjeurissen
Volume render does work for the original mask (pre dilation/smoothing/etc) and I have the exact same settings for that volume and the glass brain image.
EDIT: Solved it. I was running MRView in a singularity container and maybe it mem’d out or something. I ran it on my Windows machine and it was a bit slow but opened fine.