.. _external_pipeline:

External Pipelines
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Macaque diffusion weighted imaging
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How to create a whole brain tractogram?
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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

.. code-block:: bash

    $ 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
-------------------------------------------------
.. code-block:: bash

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



Diffusion tensor estimation
----------------------------

.. code-block:: bash

    $ dwi2tensor
      sub-xxx.mif
      tensor.mif



Maps Generation of tensor-derived parameters
---------------------------------------------

.. code-block:: bash

    $ 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


.. code-block:: bash

    $ 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

.. code-block:: bash

    $ 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
-----------------------------------------

.. code-block:: bash

    $ 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)

.. code-block:: bash

    $ 5tt2gmwmi
      gen_5tt.nii
      gmwmSeed.mif



Perform streamlines tractography
--------------------------------

.. code-block:: bash

    $ 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
------------------------------

.. code-block:: bash

    $ 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
---------------------------------------------------------------------------------------------------

.. code-block:: bash

    $ 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
-------------------------------------------------------

.. code-block:: bash

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

Option: -linear: specify a linear transform to apply