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7 | 7 | As of FMRIPREP 1.0.12, the software includes a tracking system |
8 | 8 | to report usage statistics and errors. Users can opt-out using |
9 | 9 | the ``--notrack`` command line argument. |
10 | | - |
| 10 | + |
11 | 11 |
|
12 | 12 | Execution and the BIDS format |
13 | 13 | ============================= |
@@ -38,6 +38,110 @@ Command-Line Arguments |
38 | 38 | :nodefaultconst: |
39 | 39 |
|
40 | 40 |
|
| 41 | +.. _output-spaces: |
| 42 | + |
| 43 | +Defining standard and nonstandard spaces where data will be resampled |
| 44 | +===================================================================== |
| 45 | + |
| 46 | +The command line interface of fMRIPrep allows resampling the preprocessed data |
| 47 | +onto other output spaces. |
| 48 | +That is achieved using the ``--output-spaces`` argument, where standard and |
| 49 | +nonstandard spaces can be inserted. |
| 50 | + |
| 51 | +Standard spaces |
| 52 | +""""""""""""""" |
| 53 | + |
| 54 | +When using fMRIPrep in a workflow that will investigate effects that span across |
| 55 | +analytical groupings, neuroimagers typically resample their data on to a standard, |
| 56 | +stereotactic coordinate system. |
| 57 | +The most extended standard space for fMRI analyses is generally referred to MNI. |
| 58 | +For instance, to instruct fMRIPrep to use the MNI template brain distributed with |
| 59 | +FSL as coordinate reference the option will read as follows: ``--output-spaces MNI152NLin6Asym``. |
| 60 | +By default, fMRIPrep uses ``MNI152NLin2009cAsym`` as spatial-standardization reference. |
| 61 | +Valid template identifiers (``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, etc.) come from |
| 62 | +the `TemplateFlow project <https://github.com/templateflow/templateflow>`__. |
| 63 | + |
| 64 | +Therefore, fMRIPrep will run nonlinear registration processes against the template |
| 65 | +T1w image corresponding to all the standard spaces supplied with the argument |
| 66 | +``--output-spaces``. |
| 67 | +By default, fMRIPrep will resample the preprocessed data on those spaces (labeling the |
| 68 | +corresponding outputs with the `space-<template-identifier>` BIDS entity) but keeping |
| 69 | +the original resolution of the BOLD data to produce smaller files, more consistent with |
| 70 | +the original data gridding. |
| 71 | +However, many users will be interested in utilizing a coarse gridding (typically 2mm isotropic) |
| 72 | +of the target template. |
| 73 | +Such a behavior can be achieved applying modifiers to the template identifier, separated by |
| 74 | +a ``:`` character. |
| 75 | +For instance, ``--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym`` will generate |
| 76 | +preprocessed BOLD 4D files on two standard spaces (``MNI152NLin6Asym``, |
| 77 | +and ``MNI152NLin2009cAsym``) with the template's 2mm isotropic resolution for |
| 78 | +the data on ``MNI152NLin6Asym`` space and the original BOLD resolution |
| 79 | +(say, e.g., 2x2x2.5 [mm]) for the case of ``MNI152NLin2009cAsym``. |
| 80 | + |
| 81 | +Other possible modifiers are, for instance, the ``cohort`` selector. |
| 82 | +Although currently there is no template in TemplateFlow with several cohorts, |
| 83 | +very soon we will integrate pediatric templates, for which ``cohort`` will |
| 84 | +function to select the appropriate age range. |
| 85 | +Therefore, in upcoming versions of fMRIPrep, it will be possible to run it with |
| 86 | +``--output-spaces MNIPediatricAsym:res-2:cohort-2`` where ``cohort-2`` would select |
| 87 | +the template instance for the, say, 24-48 months old range. |
| 88 | + |
| 89 | +When specifying surface spaces (e.g., ``fsaverage``), the legacy identifiers from |
| 90 | +FreeSurfer will be supported (e.g. ``fsaverage5``) although the use of the density |
| 91 | +modifier would be preferred (i.e. ``fsaverage:den-10k`` for ``fsaverage5``). |
| 92 | + |
| 93 | +Custom standard spaces |
| 94 | +"""""""""""""""""""""" |
| 95 | + |
| 96 | +Although the functionality is not available yet, the interface of the |
| 97 | +``--output-spaces`` permits providing paths to custom templates that |
| 98 | +follow TemplateFlow's naming conventions |
| 99 | +(e.g. ``/path/to/custom/templates/tpl-MyCustom:res-2``). |
| 100 | +Following the example, at least the following files |
| 101 | +must be found under under ``/path/to/custom/templates/tpl-MyCustom``: :: |
| 102 | + |
| 103 | + tpl-MyCustom/ |
| 104 | + template_description.json |
| 105 | + tpl-MyCustom_res-1_T1w.nii.gz |
| 106 | + tpl-MyCustom_res-1_desc-brain_mask.nii.gz |
| 107 | + tpl-MyCustom_res-2_T1w.nii.gz |
| 108 | + tpl-MyCustom_res-2_desc-brain_mask.nii.gz |
| 109 | + |
| 110 | +Although a more comprehensive coverage of standard files would be advised. |
| 111 | + |
| 112 | +Nonstandard spaces |
| 113 | +"""""""""""""""""" |
| 114 | + |
| 115 | +Additionally, ``--output-spaces`` accepts identifiers of spatial references |
| 116 | +that do not generate *standardized* coordinate spaces: |
| 117 | + |
| 118 | + * ``T1w`` or ``anat``: data are resampled into the individual's anatomical |
| 119 | + reference generated with the T1w and T2w images available within the |
| 120 | + BIDS structure. |
| 121 | + * ``fsnative``: similarly to the ``anat`` space for volumetric references, |
| 122 | + including the ``fsnative`` space will instruct fMRIPrep to sample the |
| 123 | + original BOLD data onto FreeSurfer's reconstructed surfaces for this |
| 124 | + individual. |
| 125 | + * **Additional nonstandard spaces** that will be supported in the future are |
| 126 | + ``run``, ``func``, and ``sbref``. |
| 127 | + |
| 128 | +Modifiers are not allowed when providing nonstandard spaces. |
| 129 | + |
| 130 | +Preprocessing blocks depending on standard templates |
| 131 | +"""""""""""""""""""""""""""""""""""""""""""""""""""" |
| 132 | + |
| 133 | +Some modules of the pipeline (e.g. the ICA-AROMA denoising, the generation of |
| 134 | +HCP compatible *grayordinates* files, or the *fieldmap-less* distortion correction) |
| 135 | +operate in specific template spaces. |
| 136 | +When selecting those modules to be included (using any of the following flags: |
| 137 | +``--use-aroma``, ``--cifti-outputs``, ``--use-syn-sdc``) will modify the list of |
| 138 | +output spaces to include the space identifiers they require, should the |
| 139 | +identifier not be found within the ``--output-spaces`` list already. |
| 140 | +In other words, running fMRIPrep with ``--output-spaces MNI152NLin6Asym:res-2 |
| 141 | +--use-syn-sdc`` will expand the list of output spaces to be |
| 142 | +``MNI152NLin6Asym:res-2 MNI152NLin2009cAsym``. |
| 143 | + |
| 144 | + |
41 | 145 | The docker wrapper CLI |
42 | 146 | ====================== |
43 | 147 |
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@@ -85,7 +189,7 @@ make your data available within that system first. |
85 | 189 |
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86 | 190 | For instance, here at the Poldrack Lab we use Stanford's |
87 | 191 | :abbr:`HPC (high-performance computing)` system, called Sherlock. |
88 | | -Sherlock enables `the following data transfer options |
| 192 | +Sherlock enables `the following data transfer options |
89 | 193 | <https://www.sherlock.stanford.edu/docs/user-guide/storage/data-transfer/>`_. |
90 | 194 |
|
91 | 195 | Alternatively, more comprehensive solutions such as `Datalad |
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