diff --git a/docs/license.rst b/docs/license.rst index 137f00e..d5aece8 100644 --- a/docs/license.rst +++ b/docs/license.rst @@ -8,8 +8,7 @@ License information ------------------- Copyright (c) the *NiPreps* Developers. -As of the 21.0.x pre-release and release series, *fMRIPost-AROMA* is -licensed under the Apache License, Version 2.0 (the "License"); +*fMRIPost-AROMA* is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 @@ -23,9 +22,4 @@ limitations under the License. Copyright (c), the *fMRIPost-AROMA* developers and the CRN. All rights reserved. -*fMRIPost-AROMA* 20.2 series and earlier are -licensed under the BSD 3-clause license. -You may obtain a copy of the License at -https://opensource.org/licenses/BSD-3-Clause - All trademarks referenced herein are property of their respective holders. diff --git a/docs/outputs.rst b/docs/outputs.rst index 908c0ff..523e40c 100644 --- a/docs/outputs.rst +++ b/docs/outputs.rst @@ -95,116 +95,6 @@ Preprocessed, or derivative, data are written to ``/sub-/``. The `BIDS Derivatives`_ specification describes the naming and metadata conventions we follow. -Anatomical derivatives -~~~~~~~~~~~~~~~~~~~~~~ -Anatomical derivatives are placed in each subject's ``anat`` subfolder:: - - sub-/ - anat/ - sub-[_space-]_desc-preproc_T1w.nii.gz - sub-[_space-]_desc-preproc_T2w.nii.gz - sub-[_space-]_desc-brain_mask.nii.gz - sub-[_space-]_dseg.nii.gz - sub-[_space-]_label-CSF_probseg.nii.gz - sub-[_space-]_label-GM_probseg.nii.gz - sub-[_space-]_label-WM_probseg.nii.gz - -Spatially-standardized derivatives are denoted with a space label, -such as ``MNI152NLin2009cAsym``, while derivatives in -the original ``T1w`` space omit the ``space-`` keyword. - -T2w images are aligned to the anatomical (``T1w``) space, if found. - -.. note:: - - T2w derivatives are only generated if FreeSurfer processing is enabled. - -Additionally, the following transforms are saved:: - - sub-/ - anat/ - sub-_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5 - sub-_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 - -If FreeSurfer reconstructions are used, the following surface files are generated:: - - sub-/ - anat/ - sub-_hemi-[LR]_white.surf.gii - sub-_hemi-[LR]_midthickness.surf.gii - sub-_hemi-[LR]_pial.surf.gii - sub-_hemi-[LR]_desc-reg_sphere.surf.gii - sub-_hemi-[LR]_space-fsLR_desc-reg_sphere.surf.gii - sub-_hemi-[LR]_space-fsLR_desc-msmsulc_sphere.surf.gii - -The registration spheres target ``fsaverage`` and ``fsLR`` spaces. If MSM -is enabled (i.e., the ``--no-msm`` flag is not passed), then the ``msmsulc`` -spheres are generated and used for creating ``space-fsLR`` derivatives. - -And the affine translation (and inverse) between the original T1w sampling and FreeSurfer's -conformed space for surface reconstruction (``fsnative``) is stored in:: - - sub-/ - anat/ - sub-_from-fsnative_to-T1w_mode-image_xfm.txt - sub-_from-T1w_to-fsnative_mode-image_xfm.txt - -Finally, cortical thickness, curvature, and sulcal depth maps are converted to GIFTI -and CIFTI-2:: - - sub-/ - anat/ - sub-_hemi-[LR]_thickness.shape.gii - sub-_hemi-[LR]_curv.shape.gii - sub-_hemi-[LR]_sulc.shape.gii - sub-_space-fsLR_den-32k_thickness.dscalar.nii - sub-_space-fsLR_den-32k_curv.dscalar.nii - sub-_space-fsLR_den-32k_sulc.dscalar.nii - -.. warning:: - - GIFTI metric files follow the FreeSurfer conventions and are not modified - by *fMRIPost-AROMA* in any way. - - The Human Connectome Project (HCP) inverts the sign of the curvature and - sulcal depth maps. For consistency with HCP, *fMRIPost-AROMA* follows these - conventions and masks the medial wall of CIFTI-2 dscalar files. - -.. _fsderivs: - -FreeSurfer derivatives -~~~~~~~~~~~~~~~~~~~~~~ -If FreeSurfer is run, then a FreeSurfer subjects directory is created in -``/sourcedata/freesurfer`` or the directory indicated with the -``--fs-subjects-dir`` flag. -Additionally, FreeSurfer segmentations are resampled into the BOLD space, -and lookup tables are provided. :: - - / - sourcedata/ - freesurfer/ - fsaverage{,5,6}/ - mri/ - surf/ - ... - sub-