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Command line parameters
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***********************
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The following parameters are mandatory
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All parameters available for `macapype <https://macatools.github.io/macapype/index.html>`_ are also available in skullTo3d. These parameters are recalled here
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* -data *like in macapype*
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the path to your data dataset (existing BIDS format directory)
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* -out *like in macapype*
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the path to the output results (an existing path)
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--------------------
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mandatory parameters
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--------------------
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* -soft *like in macapype*
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can be one of these : SPM or ANTS
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* with _skull after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed)
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* with _robustreg (at the end) to have a more robust registration (in two steps) *like in macapype*
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* with _test (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png) *like in macapype*
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* with _prep (at the end) will perform data preparation (no brain extraction and segmentation) *like in macapype*
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* with _noseg (at the end) will perform data preparation and brain extraction (no segmentation) *like in macapype*
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* with _seq (at the end) to run in sequential mode (all iterables will be processed one after the other; equivalent to -nprocs 1) *like in macapype*
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* ``-data`` : path to your data dataset (existing BIDS format directory)
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* ``-out`` : path to the output results (an existing path)
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* ``-soft`` : can be one of these : SPM or ANTS ( **NB:** SPM requires a specific version of macapype/skullTo3d, not available by default)
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For ``-soft`` value, it is possible to add some key words (e.g. ``-soft ANTS_robustreg_prep``) all these options are available (to place after SPM or ANTS, e.g) and will change the brain extraction:
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**Note** : _skullnoisypetra instead of _skull available for macaque with issues on petra
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* ``_4animal`` : will use bet4animal (FSL) for brain extraction, for faster computation (by default atlas_brex is used)
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* ``_quick`` : will use hd-bet (Deep Learning) for brain extraction, for faster computation (by default atlas_brex is used)
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**NB: ** hd-bet requires a specific version of macapype/skullTo3d, not available by default
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The following parameters are exclusive
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This option should be used if the coregistration to template in preparation is not performed correctly:
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* ``_robustreg`` (at the end) to have a more robust registration (in two steps)
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Finally, these option are available (to place after SPM or ANTS) and will modify the parameters but can be launched in sequence:
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* ``_test`` : (at the end) to check if the full pipeline is coherent (will only generate the graph.dot and graph.png)
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* ``_prep`` (at the end) will perform data preparation (no brain extraction and segmentation)
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* ``_noseg`` (at the end) will perform data preparation and brain extraction (no segmentation)
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**Some options are specific to skullTo3d:**
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* ``_skull`` after SPM or ANTS if you want to process skull or angio *specific to skullTo3d*; otherwise the main pipelines of macapype will be launched (only brain segmentation will be performed) **NB : ** ``_skullnoisypetra`` instead of ``_skull`` available for macaque with issues on petra
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* ``_noskullmask`` (at the end) will perform realignement to stereo and headmask (only realignement for CT)
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* ``_noheadmask`` (at the end) will perform only realignement to stereo
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--------------------
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exclusive parameters
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--------------------
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*(but one is mandatory)*
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* -params *(mandatory if -species is omitted)*
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a json file specifiying the global parameters of the analysis. See :ref:`Parameters <params>` for more details
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* ``-params`` : *(mandatory if -species is omitted)* a json file specifiying the global parameters of the analysis. See :ref:`Parameters <params>` for more details
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* ``-species`` : *(mandatory if -params is omitted)* followed the NHP species corresponding to the image, e.g. {macaque | marmo | baboon | chimp}
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* -species *(mandatory if -params is omitted)*
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followed the NHP species corresponding to the image, e.g. {macaque | marmo | baboon | chimp}
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**NB** marmoT2 can be used for segmenting from the T2w image (by default, T1w is used for marmo)
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**NB** macaque_0p5 is available to use downsampled template (faster results)
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In extra, marmoT2 can be used for segmenting from the T2w image (by default, T1w is used)
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--------------------------------------
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The following parameters are optional
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-------------------
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optional parameters
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-------------------
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*(but highly recommanded)*
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* -brain_dt *equivalent to -dt in macapype*
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* ``-brain_dt`` *equivalent to -dt in macapype*
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specifies the datatype available to perform brain segmentation (can be "T1", or "T1 T2").
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**Note** : default is T1 if the attribute is omitted
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* -skull_dt *specific to skullTo3d*
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**NB** : default is T1 if the attribute is omitted
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* ``-skull_dt`` *specific to skullTo3d*
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specifies the datatype available for skull segmentation (can be, "T1", "petra", "CT", "angio" or a combination of the latter (with space(s) in between).
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**Note** : default is T1 if the attribute is omitted.
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* -deriv creates a derivatives directory, with all important files, properly named following BIDS derivatives convertion
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**NB** : default is T1 if the attribute is omitted.
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* ``-deriv`` : creates a derivatives directory, with all important files, properly named following BIDS derivatives convertion. See :ref:`Derivatives <derivatives>` for a descrition of the outputs
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* ``-padback`` : exports most important files in native (original) space
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------------------------
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more optional parameters
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------------------------
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* ``-indiv`` or ``-indiv_params`` : a json file overwriting the default parameters (both macapype default and parameters specified in -params json file) for specific subjects/sessions. See :ref:`Individual Parameters <indiv_params>` for more details
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* ``-sub`` (-subjects), ``-ses`` (-sessions), ``-acq`` (-acquisions), ``-rec`` (-reconstructions) allows to specifiy a subset of the BIDS dataset respectively to a range of subjects, session, acquision types and reconstruction types. The arguments can be listed with space seperator. **Note** if not specified, the full BIDS dataset will be processed
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* ``-nprocs`` : an integer, to specifiy the number of processes that should be allocated by the parralel engine of macapype
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* typically equals to the number of subjects*session (i.e. iterables).
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* can be multiplied by 2 if T1*T2 pipelines are run (the first steps at least will benefit from it)
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* default = 4 if unspecified ; if is put to 1, then the sequential processing is used
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* ``-mask`` allows to specify a precomputed binary mask file (skipping brain extraction). The best usage of this option is: precomputing the pipeline till brain_extraction_pipe, modify by hand the mask and use the mask for segmentation. Better if only one subject*session is specified (one file is specified at a time...).
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**Warning:** the mask should be in the same space as the data. And only works with -soft ANTS so far
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* -pad exports (in derivatives) important files in native (original) space
Depending on the options provided by command line and params.json, different files will ouput
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Derivatives will be output if option ``-deriv`` is provided to the command line (See `Commands <command>`_):
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All files are by default in stereo space; if option ``-padback`` is provided to the command line (See `Commands <command>`), files in native will also be output.
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For all files provided by macapype, see `Derivatives <https://macatools.github.io/macapype/derivatives.html>`_ and see `Derivatives <https://macatools.github.io/macapype/derivatives.html>`_
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Data Preparation (Padded files)
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*******************************
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**If pad_template is defined in params (normalily used to coregister stereo to petra, T1w and CT):**
**NB** if pad_template is defined (as normally is by default in all skullTo3d parameter files...) , stereo corresponds to desc-pad files for macapype processing.
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