Freesurfer学习笔记——Troubleshooting your output（输出故障排除）3/13

准备工作：

## bash
export FREESURFER_HOME=/path/to/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export TUTORIAL_DATA=<path_to_your_tutorial_data>
export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

## tcsh
setenv FREESURFER_HOME /path/to/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv TUTORIAL_DATA <path_to_your_tutorial_data>
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

 

The white matter surface：白质和灰质的界限

The pial surface（软脑膜表面）：灰质和脑脊液的界限

手工检查：

1. white surface 是否沿着白质和灰质的界限

2. 皮质下分割是否遵循强度边界

 

常见错误：

1. Skull Strip Errors
2. Segmentation Errors
3. Intensity Normalization Error
4. Pial Surface misplacement
5. Topological Defect

常见解决办法：

1. Erase voxels
2. Fill voxels
3. Clone voxels (ie, copy from one volume to another)
4. Add “Control Points”

 

Edits to the brainmask volume (pial surface error)

打开pial_edits_before中的文件：

freeview -v  pial_edits_before/mri/T1.mgz  \
pial_edits_before/mri/brainmask.mgz  \
-f pial_edits_before/surf/lh.white:edgecolor=yellow \
pial_edits_before/surf/lh.pial:edgecolor=red \
pial_edits_before/surf/rh.white:edgecolor=yellow \
pial_edits_before/surf/rh.pial:edgecolor=red

更正方法

打开更正后的文件pial_edits_after：

freeview -v  pial_edits_after/mri/T1.mgz  \
pial_edits_after/mri/brainmask.mgz  \
-f pial_edits_after/surf/lh.white:edgecolor=yellow \
pial_edits_after/surf/lh.pial:edgecolor=red \
pial_edits_after/surf/rh.white:edgecolor=yellow \
pial_edits_after/surf/rh.pial:edgecolor=red

Edits to the wm volume (segmentation error)

打开wm1_edits_before中的文件：

freeview -v wm1_edits_before/mri/brainmask.mgz \
wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 \
-f wm1_edits_before/surf/lh.white:edgecolor=yellow \
wm1_edits_before/surf/lh.pial:edgecolor=red \
wm1_edits_before/surf/rh.white:edgecolor=yellow \
wm1_edits_before/surf/rh.pial:edgecolor=red \
wm1_edits_before/surf/rh.inflated:visible=0 \
wm1_edits_before/surf/lh.inflated:visible=0

更正方法

打开更正后的文件wm1_edits_after：

freeview -v wm1_edits_after/mri/T1.mgz  \
wm1_edits_after/mri/brainmask.mgz  \
-f wm1_edits_after/surf/lh.white:edgecolor=yellow \
wm1_edits_after/surf/lh.pial:edgecolor=red \
wm1_edits_after/surf/rh.white:edgecolor=yellow \
wm1_edits_after/surf/rh.pial:edgecolor=red

Correcting topological defects (white surface error)

打开topo_defect_before中的文件：

freeview -v topo_defect_before/mri/brainmask.mgz \
topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4 \
-f topo_defect_before/surf/lh.white:edgecolor=yellow \
topo_defect_before/surf/lh.pial:edgecolor=red \
topo_defect_before/surf/rh.white:edgecolor=yellow \
topo_defect_before/surf/rh.pial:edgecolor=red

更正方法

打开更正后的文件topo_defect_after：

freeview -v topo_defect_after/mri/brainmask.mgz \
topo_defect_after/mri/wm.mgz:colormap=heat:opacity=0.4 \
-f topo_defect_after/surf/lh.white:edgecolor=yellow \
topo_defect_after/surf/lh.pial:edgecolor=red \
topo_defect_after/surf/rh.white:edgecolor=yellow \
topo_defect_after/surf/rh.pial:edgecolor=red

Skull strip

颅骨剥离后，比较brainmask.mgz和T1.mgz来检查头骨是否完全剥离，只留下完整的皮质和小脑。

打开t​​​​​​​skullstrip_before中的文件：

freeview -v skullstrip_before/mri/T1.mgz \
skullstrip_before/mri/brainmask.mgz:visible=false \
-f skullstrip_before/surf/lh.white:edgecolor=yellow \
skullstrip_before/surf/lh.pial:edgecolor=red \
skullstrip_before/surf/rh.white:edgecolor=yellow \
skullstrip_before/surf/rh.pial:edgecolor=red

更正方法

打开更正后的文件tskullstrip_after：

freeview -v skullstrip_after/mri/T1.mgz \
skullstrip_after/mri/brainmask.mgz \
-f skullstrip_after/surf/lh.white:edgecolor=yellow \
skullstrip_after/surf/lh.pial:edgecolor=red \
skullstrip_after/surf/rh.white:edgecolor=yellow \
skullstrip_after/surf/rh.pial:edgecolor=red

Adding control points (intensity normalization error)强度归一化问题

检查white surface，如果有白质没有被包括在内的地方，则此时brainwask体素强度应处于或非常接近110，否则应修改。

打开​​​​​​​cp_before中的文件：

freeview -v cp_before/mri/brainmask.mgz \
cp_before/mri/T1.mgz \
-f cp_before/surf/lh.white:edgecolor=blue \
cp_before/surf/lh.pial:edgecolor=red \
cp_before/surf/rh.white:edgecolor=blue \
cp_before/surf/rh.pial:edgecolor=red

更正方法

打开更正后的文件cp_after：

freeview -v cp_after/mri/brainmask.mgz \
cp_after/mri/T1.mgz \
-f cp_after/surf/lh.white:edgecolor=blue \
cp_after/surf/lh.pial:edgecolor=red \
cp_after/surf/rh.white:edgecolor=blue \
cp_after/surf/rh.pial:edgecolor=red

Less common errors (Talairach, Aseg)

Editing the Aseg：首先建议使用xopts脚本来更改正在使用的强度阈值，最后在手动更改。

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Implementing fixes

Processing stream overview

Frequently used commands

If you've made edits to the brainmask volume and would like to re-create the pial surface, run:

recon-all -autorecon-pial -subjid <subject>

If you've made edits to the white matter volume (segmentation error or topological error) and would like to re-create final surfaces, run:

recon-all -autorecon2-wm -autorecon3 -subjid <subject>

If you've added control points:

recon-all -autorecon2-cp -autorecon3 -subjid <subject>

If you cannot remember which command to run, use the -make flag. Recon-all will automatically begin at whichever point in the processing stream you made your edits. Note: please see below under "Tips and general questions" for information on running with v6.0.

recon-all -make all -subjid <subject>

If you have corrected several types of errors, it is recommended that you re-run recon-all from the beginning, to ensure that none of your edits were left out. (Running from autorecon1 will not save you much time)

recon-all -all -subjid <subject>

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How do you know which volumes to edit?

如果pail surface包含多出来的部分，应编辑brainmask.mgz；如果white surface错误或者pial surface包含的缺少了(分割错误)，应编辑wm.mgz；如果归一化错误则应增加control point；这是因为pail surface的错误通常是由white surface的潜在错误引起的。

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