[備份] MNE 分析流程

1. Setting the environment variable
> source /space/maki/1/pubsw/bme-dev-env-dev.csh
2. setup the macro of subjects' anatomy data
> setenv SUBJECTS_DIR XXXXXX
3. setup the subject's name (the one to be analyzed)
> setenv SUBJECT XXXX
4. Follow the instructions from MNE guide 3.4

Note:
1. To establish symbolic link: (for example)
> ln -s ./watershed/XXX.surf inner_skull.surf
2. To align the coordinate in mrilab (To use mrilab, always connect to maki.bm.ntu.edu.tw first)
> /neuro/bin/vue/mrilab &


%1%unpack MRI file
source /space/maki/1/pubsw/bme-dev-env-dev.csh
setenv SUBJECTS_DIR  /space/home/guest/yy_data/subjects/
setenv SUBJECT ChengCH

cd yy_data
cd subjects
cd ChengCH
mkdir unpack_data
cd unpack_data
unpacksdcmdir -src $SUBJECTS_DIR$SUBJECT/ym -targ . -scanonly ./info
vi unpack.rule
unpacksdcmdir -src $SUBJECTS_DIR$SUBJECT/ym -targ . -cfg ./unpack.rule

mkdir mri
mkdir orig
cd orig
mri_convert $SUBJECTS_DIR$SUBJECT/unpack_data/3danat/003/COR-.info ./001.mgz
recon-all -subjid $SUBJECT -all

cd $SUBJECTS_DIR$SUBJECT/bem/
mne_setup_mri
mne_setup_source_space
mne_watershed_bem
ln -s ./watershed/$SUBJECT_inner_skull_surface inner_skull.surf
mne_setup_forward_model --surf --homog

vi bad.txt
mne_mark_bad_channels --bad bad.txt raw_Aud_simple_50ms_01.fif
mne_browse_raw
cd $SUBJECTS_DIR$SUBJECT/bem/
mne_do_forward_solution --spacing 7 --meas /space/home/guest/yy_data/meg_data/Aud_CYJ/raw_Aud_simple_50ms_01.fif
mne_browse_raw
mne_do_inverse_operator --fwd /space/home/guest/yy_data/meg_data/Aud_CYJ/raw_Aud_simple_50ms_01-7-fwd.fif --loose 0.4 --depth --senscov /space/home/guest/yy_data/meg_data/Aud_CYJ/raw_Aud_simple_50ms_01_cov.fif


範例:
source /space/maki/1/pubsw/bme-dev-env-dev.csh

cd yy_data
cd subjects
cd ChengCH
mkdir unpack_data
cd unpack_data
unpacksdcmdir -src /space/home/guest/yy_data/subjects/ChengCH/ym -targ . -scanonly ./info
vi unpack.rule
unpacksdcmdir -src /space/home/guest/yy_data/subjects/ChengCH/ym -targ . -cfg ./unpack.rule

%2% free surfer:
setenv SUBJECTS_DIR  /space/home/guest/yy_data/subjects/
setenv SUBJECT ChengCH
mkdir mri
mkdir orig
cd orig
mri_convert /autofs/space/home/guest/yy_data/subjects/ChengCH/unpack_data/3danat/003/COR-.info ./001.mgz
recon-all -subjid $SUBJECT -all

[MEG] 建立 freesurfer 使用環境

我是使用 tcsh shell

1.設定環境變數
#依序是：
#freesurfer 的根目錄
#受試者的目錄
#欲分析的受試者目錄
#MNE的根目錄
setenv FREESURFER_HOME /media/D/mne/freesurfer
setenv SUBJECTS_DIR /media/D/mne/subjects
setenv SUBJECT TsengYJ
setenv MNE_ROOT /media/D/mne/mne2.7

2.設定 path
source $FREESURFER_HOME/SetUpFreeSurfer.csh
source /media/D/mne/mne2.7/bin/mne_setup

3.轉換 dicom 格式，使 freesurfer 可以讀取
cd /media/D/mne/subjects/TsengYJ
mkdir unpack_data
cd unpack_data
# -src 是source的目錄裡面放 dicom 的檔案，
unpacksdcmdir -src $SUBJECTS_DIR$SUBJECT/dicom -targ . -scanonly ./info


#根據上面敘述，建立一個 unpack.rule 檔案, 內容類似下面的敘述
# 5 3danat COR blah

vi unpack.rule

unpacksdcmdir -src $SUBJECTS_DIR$SUBJECT/ym -targ . -cfg ./unpack.rule

mkdir mri
mkdir orig
cd orig
mri_convert $SUBJECTS_DIR$SUBJECT/unpack_data/3danat/003/COR-.info ./001.mgz

recon-all -subjid $SUBJECT -all



#等待約至少 20 小時, freesurfer 將自動重建 MRI 影像