MRtrix3

1. 경로 설정:export PATH=/Applications/mrtrix3/release/bin:$PATH

mrconvert [ options ]  input output

Dw gradient table export options 

-export_grad_mrtrix path

-export_grad_fsl bvecs bvals 

Gradient table import options

-fslgrad bvecs bvals 

Pipeline 

1. dwidenoise dti_native.nii.gz dti_denoise.mif

2. dwipreproc -rpe_none -fslgrad dti.bvec dti.bval AP dti_denoise.mif dti_preproc.nii

3. dwi2mask -fslgrad dti.bvec dti.bval dti_preproc.mif dti_mask_mrtrix.mif

(Dilated mask 만드는 법: dwi2mask -fslgrad dti.bvec dti.bval dti_preproc.mif | mask filter - dilate -npass 5 dti_mask_mrtrix.mif)  

4. dwi2response tournier -fslgrad dti.bvec dti.bval dti_preproc.mif RF.txt

5. dwi2fod csd dti_preproc.mif RF.txt dti_preproc_FOD.mif -mask dti_mask_mrtrix.mif -fslgrad dti.bvec dti.bval –force

$ tckgen <Input FOD image> <Output track file> -seed_image <Input DWI mask> -mask <Input DWI mask> -number <Number of tracks> 

6. tckgen dti_preproc_FOD.mif tracks_80000_iFOD2.tck -seed_image dti_preproc.mif -mask dti_mask_mrtrix.mif -fslgrad bvec bval -force -algorithm iFOD2 -number 80000 -nthreads 4

mask를 만들때 dilate를 쓴다. script 를 만들때 -thread 4로 속도를 올린다. (Single subject를 할 때)
sift로 valitation을 한다. 

Group으로 할 때는 하나의 response function을 만든다. 

Bias filed correction을 시행 

ants를 깔아서 bias field correction한다. (Ants install 한다. )

ANTS를 까는 법: https://brianavants.wordpress.com/2012/04/13/updated-ants-compile-instructions-april-12-2012/

$ mrview <Input DWI> -tractography.load <Output track file>

mrview dti_preproc.nii -tractography.load /Users/rehappydoc/mrtrix3_data/tracks_80000_iFOD2.tck 

tkgen - 100M
FOD 100M (sw

$ tckedit <Track file> <Smaller track file> -number <Smaller number of tracks>

$ mrview <Input DWI> -tractography.load <Smaller track file>

tckedit tracks_80000_iFOD2.tck tracks_10000_iFOD2.tck -number 10000

mrview /Users/rehappydoc/mrtrix3_data/dti_preproc.nii -tractography.load /Users/rehappydoc/mrtrix3_data/tracks_10000_iFOD2.tck 

$ tckmap <Input track file> <Output TDI> -vox <Voxel size in mm>
$ mrview <Output TDI>

$ tckmap dti_preproc_1.nii 80000_TDI_3.nii vox 1
$ mrview 80000_TDI_3.nii

7.tcksift [options] in_tracks in_fod out_tracks

tcksift tracks_100M_iFOD2.tck dti_preproc_FOD.nii out_tracks.tck 

8.. TractConverter.py –i tracks_80000_iFOD2.tck -o T80000_iFOD2.trk -a corregistered_T1_image.nii

Beginner: Connectome pipeline (Updated):

http://community.mrtrix.org/t/beginner-connectome-pipeline-updated/373