External Pipelines¶

Macaque diffusion weighted imaging¶

How to create a whole brain tractogram?¶

This pipeline call some commands of the MRtrix tool. You can find the documentation of MRtrix here : https://osf.io/pm9ba/

Perform conversion between different file types¶

Convertion of bvecs bvals and dwi.nii files in one file .mif

$ mrconvert corrected_dwi_sub-xx_ses-T1_acq-AP_dwi.nii.gz
  -fslgrad
  corrected_bvecs_sub-xxx_ses-T1_acq-AP_dwi.txt
  raw_bvals_sub-xxx_ses-T1_acq-AP_dwi.txt
  output_sub-xxx.mif

Option: -fslgrad to reimport diffusion gradient table

Generation of a whole brain mask from a DWI image¶

$ dwi2mask
  sub-xxx.mif
  sub-xxx_mask.mif

Diffusion tensor estimation¶

$ dwi2tensor
  sub-xxx.mif
  tensor.mif

Maps Generation of tensor-derived parameters¶

$ tensor2metric
  tensor.mif
  -fa
  fa.mif

Option: -fa to compute the fractional anisotropy (FA) of the diffusion tensor

Constrained spherical deconvolution (CSD)¶

Estimation of the impulsionnal response = diffusion signal produced by 1 fiber

$ dwi2response dhollander
  sub-xxx.mif
  wm.txt
  gm.txt
  csf.txt
  -voxels
  voxels.mif
  -mask
  sub-xxx_mask.mif

Option: -voxels to output an image showing the final voxel selection: -mask to provide an initial mask for response voxel selection

FOD estimation¶

Estimate fiber orientation distributions from diffusion data using spherical deconvolution

$ dwi2fod
  msmt_csd
  sub-xxx.mif
  wm.txt
  wm.mif
  gm.txt
  gm.mif
  csf.txt
  csf.mif

Convertion of the macaque T1 in .mif file¶

$ mrconvert
  sub-xxx_T1.nii
  sub-xxx_T1.mif

Generation of a volume which contain the probability to be on the gm-wm interface¶

For this step, you have to use the 5ttgen file generated by macapype. 5TT image is suitable for Anatomically-Constrained Tractography (ACT) (./test_pipeline_single_indiv_params_ants/full_ants_subpipes/brain_segment_from_mask_pipe/export_5tt_pipe/_session_01_subject_xx/export_5tt/gen_5tt.nii)

$ 5tt2gmwmi
  gen_5tt.nii
  gmwmSeed.mif

Perform streamlines tractography¶

$ tckgen
  -act
  gen_5tt.nii
  -backtrack
  -seed_gmwmi
  gmwmSeed.mif
  -select
  1000000
  wm.mif
  tracks_1M.tck

Option: -act: use the Anatomically-Constrained Tractography framework during tracking; provided image must be in the 5TT (five-tissue-type) format: -backtrack: allow tracks to be truncated and re-tracked if a poor structural termination is encountered -seed_gmwmi: seed from the grey matter - white matter interface -select: set the desired number of streamlines to be selected by tckgen

Reduction of the fibers number¶

$ tckedit
  tracks_1M.tck
  -number
  200000
  smaller_tracks_200k.tck

Option: -number: set the desired number of selected streamlines to be propagated to the output file

Estimation of the registration of two images together using a symmetric rigid transformation model¶

$ mrregister
  -type rigid
  -rigid
  T1_to_DWI.txt
  -transformed
  DWI_T1_space.mif
  fa.mif
  T1.nii

Option: -type rigid: the registration type: -rigid: the output text file containing the rigid transformation as a 4x4 matrix -transformed: image1 after registration transformed and regridded to the space of image2

Application of the spatial transformations to an image¶

$ mrtransform
  -linear
  T1_to_DWI.txt
  fa.mif
  T1_DWI_space.mif

Option: -linear: specify a linear transform to apply