.. _autotract: .. title:: Automatic Bundle Segmentation Automatic Bundle Segmentation ================================================ This section describes the integrated automatic virtual dissection of the main brain tracts based on `auto_tracto `_. This tool was implemented using ANTs registration tools. The main purpose of the script ``03_auto_tracts.sh`` is to split a tck tractogram into `35 white matter tracts `_, using already established automatic dissection protocols, which were manually tuned for optimal performance. Derived from a full brain tractogram, 35 bundles are virtually dissected using the `LANIREM protocols `_. The quality of the full brain tractogram will determine the quality of bundle separation. It is highly recommended to provide a tractogram with more than one million streamlines, and quality controlled for any errors. Strategies such as anatomically-contstrained tractography (ACT) and spherical deconvolution informed filtering of tractograms (SIFT), available in MRTrix3, should aid in obtaining such high-quality tractograms. .. image:: autotract.png :align: center .. tabs:: .. tab:: Processing steps - Non-linear (SyN) registration of the native FA map to the FA atlas (FMRIB58_FA_1mm) - Apply transformation to each bundle protocol to register them to the native FA space (DWI) - Verify stop criterion conditionals - Filter each white matter bundle according to the dissection protocols .. tab:: Usage There are two ways to run the *automatic bundle segmentation*. The first is integrated within the main script ``mica-pipe`` under the ``-SC`` module by adding a specific flag for this purpose, as shown in the following example: .. code-block:: bash :linenos: :caption: Integrated usage within ``mica-pipe -SC`` :emphasize-lines: 6 mica-pipe \ -sub \ -ses \ -out \ -bids \ -SC -autoTract \ -tracts 40M Automatic bundle segmentation can also be performed using the stand alone script ``03_auto_tracts.sh``. Note that the stand alone script requires that all inputs are in DWI space. .. code-block:: bash :linenos: :caption: Example usage for standalone script 03_auto_tracts.sh \ -tck sub-01_full_brain_tractogram.tck \ -outbase sub-01_tract \ -mask sub-01_binary_brain_mask.nii.gz \ -fa sub-01_FA_map.nii.gz \ -weights sub-01_full_brain_tractogram_weights.txt .. list-table:: :widths: 10 1000 :header-rows: 1 * - **Options** - **Description** * - ``-tck`` ``path`` - Full path to full tractogram file *tck* (ideally SIFTED) * - ``-outbase`` ``string`` - Base name for all outputs * - ``-mask`` ``path`` - Binary brain mask in the subject's DWI space * - ``fa`` ``path`` - FA map in subject's DWI space. This input is used for registration to the template Additional **optional arguments** can also be specified: .. list-table:: :widths: 10 1000 :header-rows: 1 * - **Optional argument** - **Description** * - ``-keep_tmp`` - If specific, the temporary directory will not be delted after processing is completed * - ``-tmpDir`` ``path`` - Specify location of temporary directory * - ``-minStreamlinesPerVoxel`` ``num`` - Streamlines are truncated if voxel contains less than this number of streamlines. Default is 1 * - ``-robust`` - This option to run a ROBUST registration, at the expense of more computation time * - ``-weights`` ``path`` - Use this option if you calculated a weights file from SIFT2 * - ``threads`` ``num`` - Number of threads (Default is 6) * - ``version``` - Print software version .. tab:: Outputs Directories created by this script will be in the selected ``outbase``. The outputs generated by the micapipe integrated script are located in */micapipe//dwi/auto_tract* .. parsed-literal:: dwi/auto_tract/ ├── _space-dwi_desc-iFOD2-40M-SIFT2_AC.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_AF_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_AF_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_atlas2fa.nii.gz ├── _space-dwi_desc-iFOD2-40M-SIFT2_CC_MID.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CGFP_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CGFP_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CGH_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CGH_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CG_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CGR_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CGR_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CG_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CST_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_CST_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_FA_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_FA_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_FMA.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_FMI.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_FX_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_FX_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_IFOF_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_IFOF_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_ILF_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_ILF_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_MLF_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_MLF_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_OR_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_OR_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_SLF_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_SLF_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_summary.txt ├── _space-dwi_desc-iFOD2-40M-SIFT2_TAPETUM.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_UF_L.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_UF_R.tck ├── _space-dwi_desc-iFOD2-40M-SIFT2_VOF_L.tck └── _space-dwi_desc-iFOD2-40M-SIFT2_VOF_R.tck The description (``desc-``) refers to the algorithm used to generate the tractogram (here, *iFOD2*), its number of streamlines (here, *40M*) and the filtering algorithm (here, *SIFT2*). List of names and their acronyms obtained with the integrated automatic virtual dissection of the main brain tracts based on auto_tracto: +---------+--------------------------------------+ | Acronym | Tract name | +=========+======================================+ | AC | Anterior Commissure | +---------+--------------------------------------+ | AF | Arcuate Fasciculus | +---------+--------------------------------------+ | CC_MID | Corpus Callosum middle portion | +---------+--------------------------------------+ | CGFP | Cingulum, fronto-parietal portion | +---------+--------------------------------------+ | CGH | Cingulum, parahippocampal portion | +---------+--------------------------------------+ | CG | Cingulum, whole | +---------+--------------------------------------+ | CGR | Cingulum, rostral and subgenual | +---------+--------------------------------------+ | CST | Corticospinal tract | +---------+--------------------------------------+ | FA | Frontal aslant | +---------+--------------------------------------+ | FMA | Forceps major of corpus callosum | +---------+--------------------------------------+ | FMI |Forceps minor of corpus callosum | +---------+--------------------------------------+ | FX | Fornix | +---------+--------------------------------------+ | IFOF | Inferior fronto-occipital fasciculus | +---------+--------------------------------------+ | ILF | Inferior longitudinal fasciculus | +---------+--------------------------------------+ | MLF | Middle longitudinal fasciculus | +---------+--------------------------------------+ | OR | Optic radiation | +---------+--------------------------------------+ | SLF | Superior longitudinal fasciculus | +---------+--------------------------------------+ | UF | Uncinate fasciculus | +---------+--------------------------------------+ | VOF | Vertical occipital fasciculus | +---------+--------------------------------------+