FreeSurfer使用（1）

下载数据：

curl https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz -o tutorial_data.tar.gz
tar -xzvf tutorial_data.tar.gz

英文版FreeSurfer Tutorials:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials

每次处理图像之前，定义路径

export TUTORIAL_DATA=/Users/yourname/tutorial_data/
cd $TUTORIAL_DATA
export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

load several output volumes, such as brainmask.mgz and wm.mgz; the surfaces, rh.white and lh.white; and the subcortical segmentation, aseg.mgz.

freeview -v \
good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_output/surf/lh.white:edgecolor=blue \
good_output/surf/lh.pial:edgecolor=red \
good_output/surf/rh.white:edgecolor=blue \
good_output/surf/rh.pial:edgecolor=red

Some notes on the above command line:

• good_output is the name of the subject

• The flag -v is used to open some of the most commonly used volumes including:

  • brainmask.mgz : skull-stripped volume primarily used for troubleshooting

  • wm.mgz : white matter mask also used for troubleshooting

  • aseg.mgz : subcortical segmentation loaded with its corresponding color table and at a low opacity. For more information on the subcortical segmentation, see here.

• The flag -f is used to load surfaces

  • white & pial surfaces are loaded for each hemisphere & with color indicated by 'edgecolor'

结果应该如图：

截屏2020-03-0921.48.44.png