FIRST
From hpcwiki
FIRST, FMRIb's Registration & Segmentation Tool, is a FSL application to extract some subcortical structures based on shape models. They application have 15 different subcortical structures. Official user guide
| L_Accu | Left Accumbens area | L_Amyg | Left Amygdala | L_Caud | Left Caudate Nucleus |
|---|---|---|---|---|---|
| L_Hipp | Left Hippocampus | L_Pall | Left Pallidum | L_Puta | Left Putamen |
| L_Thal | Left Thalamus | R_Accu | Right Accumbens area | R_Amyg | Right Amygdala |
| R_Caud | Right Caudate Nucleus | R_Hipp | Right Hippocampus | R_Pall | Right Pallidum |
| R_Puta | Right Putamen | R_Thal | Right Thalamus | BrStem | Brain Stem |
In order to run the tool:
[~~]$ run_first_all [options] -i <input_image> -o <output_image>
Optional arguments:
-m <method> : method must be one of auto, fast, none or a (numerical) threshold value
-b : input is already brain extracted
-s <name> : run only on one specified structure (e.g. L_Hipp) or a comma separated list (no
spaces)
-a <img2std.mat> : use affine matrix (do not re-run registration)
-3 : use 3-stage affine registration (only currently for hippocampus)
-d : do not cleanup image output files (useful for debugging)
-v : verbose output
-h : display this help message
for example to extract the left hippocampus and amygdala:
[~~]$ run_first_all -b -s L_Hipp,L_Amyg -i structural_brain.nii.gz -o structural-seg
This command executes the FIRST tool segmenting the left hippocampus and the left amygdala. In order to view this results type the following command in a terminal:
[~~]$ fslview structural_brain structural-seg-L_Hipp_first structural-seg-L_Amyg_first &
The figure illustrates the segmentation of Left Amygdala in red and Left Hippocampus in green.
