.. include:: links.rst ##################### Outputs of *QSIRecon* ##################### *QSIRecon* outputs are organized according to BIDS Derivatives standards. .. admonition:: A note on BIDS compliance *QSIRecon* attempts to follow the BIDS specification as closely as possible. However, many *QSIRecon* derivatives are not currently covered by the specification. In those instances, we attempt to follow recommendations from existing BIDS Extension Proposals (BEPs), which are in-progress proposals to add new features to BIDS. However, we do not guarantee compliance with any BEP, as they are not yet part of the official BIDS specification. Three BEPs that are of particular use in *QSIRecon* are `BEP016: Diffusion weighted imaging derivatives `_, `BEP017: Relationship & connectivity matrix data schema `_, and `BEP038: Atlas Specification `_. In cases where a derivative type is not covered by an existing BEP, we have simply attempted to follow the general principles of BIDS. If you discover a problem with the BIDS compliance of *QSIRecon*'s derivatives, please open an issue in the *QSIRecon* repository. ******************** Dataset Organization ******************** *QSIRecon* organizes its outputs as self-contained BIDS-Derivative datasets. In the output directory, you will find a derivative dataset containing anatomical and subject-space atlas files, along with the `MRtrix3-specific renumbering `_ files :: qsirecon/ dataset_description.json logs/ sub-/[ses-/] dwi/ _seg-_dseg.mif.gz _seg-_dseg.nii.gz _seg-_dseg.txt Within the output directory, you will also find a "derivatives" directory containing a separate self-contained derivatives dataset for each reconstruction method used by the reconstruction workflow. Each dataset will have its own set of HTML reports summarizing the results of the associated reconstruction method. Here is an example output structure from a reconstruction workflow with two reconstruction methods: DKI and TORTOISE:: qsirecon/ derivatives/ qsirecon-DKI/ dataset_description.json sub-[_ses-].html logs/ sub-/[ses-/] figures/ dwi/ _model-dki_param-ad_dwimap.json _model-dki_param-ad_dwimap.nii.gz _model-dki_param-ak_dwimap.json _model-dki_param-ak_dwimap.nii.gz _model-dki_param-kfa_dwimap.json _model-dki_param-kfa_dwimap.nii.gz _model-dki_param-md_dwimap.json _model-dki_param-md_dwimap.nii.gz _model-dki_param-mk_dwimap.json _model-dki_param-mk_dwimap.nii.gz _model-dki_param-mkt_dwimap.json _model-dki_param-mkt_dwimap.nii.gz _model-dki_param-rd_dwimap.json _model-dki_param-rd_dwimap.nii.gz _model-dki_param-rk_dwimap.json _model-dki_param-rk_dwimap.nii.gz _model-tensor_param-fa_dwimap.json _model-tensor_param-fa_dwimap.nii.gz # Microstructural metrics calculated if wmti is True _model-dkimicro_param-awf_dwimap.json _model-dkimicro_param-awf_dwimap.nii.gz _model-dkimicro_param-rde_dwimap.json _model-dkimicro_param-rde_dwimap.nii.gz qsirecon-TORTOISE/ dataset_description.json sub-[_ses-].html logs/ sub-/[ses-/] figures/ dwi/ _model-mapmri_param-ng_dwimap.json _model-mapmri_param-ng_dwimap.nii.gz _model-mapmri_param-ngpar_dwimap.json _model-mapmri_param-ngpar_dwimap.nii.gz _model-mapmri_param-ngperp_dwimap.json _model-mapmri_param-ngperp_dwimap.nii.gz _model-mapmri_param-pa_dwimap.json _model-mapmri_param-pa_dwimap.nii.gz _model-mapmri_param-path_dwimap.json _model-mapmri_param-path_dwimap.nii.gz _model-mapmri_param-rtap_dwimap.json _model-mapmri_param-rtap_dwimap.nii.gz _model-mapmri_param-rtop_dwimap.json _model-mapmri_param-rtop_dwimap.nii.gz _model-mapmri_param-rtpp_dwimap.json _model-mapmri_param-rtpp_dwimap.nii.gz _model-tensor_param-ad_dwimap.json _model-tensor_param-ad_dwimap.nii.gz _model-tensor_param-am_dwimap.json _model-tensor_param-am_dwimap.nii.gz _model-tensor_param-fa_dwimap.json _model-tensor_param-fa_dwimap.nii.gz _model-tensor_param-li_dwimap.json _model-tensor_param-li_dwimap.nii.gz _model-tensor_param-rd_dwimap.json _model-tensor_param-rd_dwimap.nii.gz If parcellation is enabled, the output directory will also contain an "atlases" directory containing a BIDS-Atlas dataset. See :ref:`connectivity_atlases` for more information on this output directory.