freesurfer 操作.docx

皮层厚度和表面积（surface area）——Freesurfer分析方法预备阶段：1打开终端，输入指令，打开tschtcsh setenv FREESURFER_HOME /usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv TUTORIAL_DATA /media/8498B05D98B05002/DATA/fs-cyh setenv SUBJECTS_DIR $TUTORIAL_DATA cd $SUBJECTS_DIR2Recon-allrecon-all \ -i one slice in the anatomical dicom series \ -s subject id that you make up \ -sd directory to put the subject folder in \ -all recon-all -i -s study -all 文件 文件夹名配准tkregister2 --mgz --s study1 --fstal --surf orig 查看看分割结果tkmedit cyh brainmask.mgz -aux T1.mgz -surfs -aseg 看膨胀结果tksurfer cyh lh inflated 在Freesurfer中，经过recon-all指令预处理，一些统计数据已经产生。他们保存在每个被试的stas/子文件夹下。有subcortical segmentation (aseg)皮层下组织分割的，还有?cortical parcellation (aparc)皮层分割的结果。一、单被试分析1.aparc.stats是不同皮层区域的统计信息，这些信息存储在lh.aparc.stats和rh.aparc.stats中。cd $SUBJECTS_DIR/cyh/statsless lh.aparc.stats（1）通过上面的命令行可以得到Structure Name,?Number of Vertices,?Surface Area,?Gray Matter Volume,?Average Thickness,Thickness StDev,?Integrated Rectified Mean Curvature,?Integrated Rectified Gaussian Curvature,?Folding Index?and?Intrinsic Curvature Indexfor each entry in the table.（2）要得到某个指定区域的统计信息，可参照Q. I am trying to measure the cortical thickness of specific ROI, how can I do this?A: You can save the ROI to a label file and then use:mris_anatomical_stats -l label file（3）要计算全脑平均厚度，参照Q. I am trying to measure the global mean cortical thickness (i.e combined across hemispheres), how would I do this?A: One suggestion is to use the surface area of each hemisphere as the weighting factor. In which case the global mean thickness including both hemispheres would be given by:bh.thickness = ( (lh.thickness * lh.surfarea) + (rh.thickness * rh.surfarea) ) / (lh.surfarea + rh.surfarea)If you use the values in the ?h.aparc.stats, it already factors out the unknown region, so you dont have to do it yourself.2.aseg.stats皮层下组织的统计数据cd $SUBJECTS_DIR/004/statsless aseg.stats通过这个命令可以得到：Segmentation Id,?Number of Voxels,?Volume,?Structure Name,?