-
Notifications
You must be signed in to change notification settings - Fork 6
Pipeline
This pipeline represente the forward method for the data analysis, by the inverse method, of an electroencephalogram.
The forward method consists of three steps. The first is to produce Fijee's input files. The second step comes to run the fijee's core executable software. And the last step is the evaluation of the electric potential on the scalp for a serie of electric dipoles.
Many Fijee's input files are produced by software (FreeSurfer, FSL, MNE, ...) based on the Freesurfer's directory tree. Also Fijee is based on Freesurfer's directory.
export PATH=$FREESURFER_HOME/bin:$PATH
export SUBJECTS_DIR=/home/ycobigo/subjects
export SUBJECT=GazzDCS0004mgh
# data names:
export DICOM=/data/dicom/tDCS/GazzDCS0004mgh/Hough/MEMPRAGE_4e_p2_1mm_isoRMS_12/
export NIFTI=/data/nifti/tDCS/GazzDCS0004mgh/
export T1=MEMPRAGE4ep21mmisos012a1001.nii.gz
export T2=T2SPACE1mmisos015a1001.nii.gz
source $FREESURFER_HOME/SetUpFreeSurfer.sh
source $MNE_ROOT/bin/mne_setup_sh $FREESURFER_HOME/bin/recon-all -subjid $SUBJECT -i $DICOM/IM-0012-0001.dcm -sd $SUBJECTS_DIR/ -all >& FreeSurfer.log &
tail -f FreeSurfer.log$SUBJECTS_DIR/$SUBJECT/surf/
mris_convert rh.pial rh.pial.{vtk, ... }
for i in rh.pial lh.pial rh.smoothwm lh.smoothwm ; do mris_convert $i VTK/$i.vtk ; doneConversion of allsegmentation file
mri_convert aseg.mgz aseg.nii.gztkregister2 --targ orig --mov dicom --regheader --reg register.dat
#
tkregister2 --targ aseg.nii.gz --mov $NIFTI/$T2 --regheader --reg register.dat
#
tkregister2 --reg register.dat --mov $NIFTI/$T1 --regheader --targ ../orig.mgz
tkregister2 --reg register.dat --targ $NIFTI/$T1 --regheader --mov ../orig.mgz
#
tkregister2 --reg T1register.dat --targ ../orig.mgz --regheader --mov $NIFTI/$T1
tkregister2 --reg T2register.dat --targ ../orig.mgz --regheader --mov $NIFTI/$T2
mri_vol2vol --in orig --out orig.dicomspace.img --temp dicom --xfm register.dat
#
mri_vol2vol --mov aseg.nii.gz --o aseg.dicomspace.nii.gz --targ $NIFTI/$T2 --xfm register.dat
#
mri_vol2vol --mov aseg.nii.gz --o aseg.dicomspace.nii.gz --targ $NIFTI/$T1 --reg register.dat
mri_vol2vol --mov aseg.nii.gz --o aseg.dicomspace.nii.gz --targ $NIFTI/$T1 --reg register.dat
#
mri_vol2vol --mov $NIFTI/$T1 --reg T1register.dat --targ ../orig.mgz --o T1FunctionalSpace.nii.gz
mri_vol2vol --mov $NIFTI/$T2 --reg T2register.dat --targ ../orig.mgz --o T2FunctionalSpace.nii.gztkregister2 --targ $SUBJECTS_DIR/$SUBJECT/mri/aseg.mgz --mov ../eigval0000.nii.gz --regheader --reg ToAseg.dat
#
mri_vol2vol --mov ../eigvals.nii --o eigvals_aseg_ref.nii --targ ~/subjects/$SUBJECT/mri/aseg.nii.gz --reg ToAseg.dat
mri_vol2vol --mov ../eigvec1.nii --o eigvec1_aseg_ref.nii --targ ~/subjects/$SUBJECT/mri/aseg.nii.gz --reg ToAseg.dat
mri_vol2vol --mov ../eigvec2.nii --o eigvec2_aseg_ref.nii --targ ~/subjects/$SUBJECT/mri/aseg.nii.gz --reg ToAseg.dat
mri_vol2vol --mov ../eigvec3.nii --o eigvec3_aseg_ref.nii --targ ~/subjects/$SUBJECT/mri/aseg.nii.gz --reg ToAseg.dat MNE Registration is required in order to download the MNE software: download.
$SUBJECTS_DIR/$SUBJECT/bem/msh-7-src.fif.mne_watershed_bem -atlas
cd $SUBJECTS_DIR/$SUBJECT/bem/
for i in GazzDCS0004mgh_brain_surface GazzDCS0004mgh_inner_skull_surface GazzDCS0004mgh_outer_skin_surface GazzDCS0004mgh_outer_skull_surface ; do mris_convert $i NIFTI/$i.nii ; done Directory organisation
cd $SUBJECTS_DIR/$SUBJECT
ln -s /data/dicom/tDCS/GazzDCS0004mgh/Hough/MEFLASH_8e_1mm_iso_5deg_7/ FLASH_5deg
ln -s /data/dicom/tDCS/GazzDCS0004mgh/Hough/MEFLASH_8e_1mm_iso_30deg_3/ FLASH_30deg
mkdir MNE_FLASH_5deg MNE_FLASH_30deg
cd MNE_FLASH_5deg
source $PATH/mne_organize_dicom ../FLASH_5deg
cd ../MNE_FLASH_30deg
source $PATH/mne_organize_dicom ../FLASH_30deg
ln -s MNE_FLASH_5deg/007_MEFLASH_8e_1mm_iso_5deg/ flash05
ln -s MNE_FLASH_30deg/003_MEFLASH_8e_1mm_iso_30deg/ flash30
source /usr/local/MNE/bin/mne_flash_bemdt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti
export DICOM_DATA=/data/nifti/tDCS/GazzDCS0004mgh/
dt_recon --i $DICOM_DATA/ep2dadvdiff511Eb200064dirs019a001.nii.gz --s $SUBJECT --o $SUBJECTS_DIR/$SUBJECT/Diffusion_tensor/ --b $DICOM_DATA/ep2dadvdiff511Eb200064dirs019a001.bval $DICOM_DATA/ep2dadvdiff511Eb200064dirs019a001.bvecfslsplit eigvals.nii eigvalThis will give you three volumes: eigval0000.nii.gz - Axial/Parallel Diffusivity. Mean of the volumes below gives you Radial/perpendicular diffusivity
# eigval0001.nii.gz # eigval0002.nii.gz
mv eigval0000.nii.gz Axial_Diffusivity.nii.gzTo get the radial diffusivity you have to get the mean of the other two eigen values:
fslmaths eigenval0001.nii.gz -add eigval0002.nii.gz -div 2 Radial_Diffisivity.nii.gz"tkregister2 --targ $SUBJECTS_DIR/GazzDCS0004mgh/mri/aseg.mgz --mov ../eigval0000.nii.gz --regheader --reg ToAseg.dat"
tkregister2 --targ $SUBJECTS_DIR/GazzDCS0004mgh/mri/orig.mgz --mov ../eigval0000.nii.gz --regheader --reg ToOrig.dat
tkregister2 --targ $SUBJECTS_DIR/GazzDCS0004mgh/mri/aseg.mgz --mov ../eigvec1.nii --regheader --reg Vec1ToAseg.dathttps://surfer.nmr.mgh.harvard.edu/fswiki/trac-all generates output files for each subject under a directory that is denoted by $SUBJECTS_DIR/<subjid></subjid>
trac-all -[step] -s <subjectname> --i <dicomfile> trac-all -[step] -c <configfile>
/home/ycobigo/Data/trac_all.config
#export DICOM_DATA=/data/nifti/tDCS/GazzDCS0004mgh/ #trac-all -s $SUBJECT -nocorr -intra -inter -nomasks -tensor -noprior -i $DICOM_DATA/ep2dadvdiff511Eb200064dirs019a001.nii.gz trac-all -nocorr -intra -inter -nomasks -tensor -noprior -c trac_all.config
The FEniCS Project is a collaborative project for the development of innovative concepts and tools for automated scientific computing, with a particular focus on automated solution of differential equations by finite element methods.