Outputs of QSIRecon

QSIRecon outputs are organized according to BIDS Derivatives standards.

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-<label>/[ses-<label>/]
      dwi/
         <source_entities>_seg-<atlas>_dseg.mif.gz
         <source_entities>_seg-<atlas>_dseg.nii.gz
         <source_entities>_seg-<atlas>_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-<label>[_ses-<label>].html
         logs/
         sub-<label>/[ses-<label>/]
            figures/
            dwi/
               <source_entities>_model-dki_param-ad_dwimap.json
               <source_entities>_model-dki_param-ad_dwimap.nii.gz
               <source_entities>_model-dki_param-ak_dwimap.json
               <source_entities>_model-dki_param-ak_dwimap.nii.gz
               <source_entities>_model-dki_param-kfa_dwimap.json
               <source_entities>_model-dki_param-kfa_dwimap.nii.gz
               <source_entities>_model-dki_param-md_dwimap.json
               <source_entities>_model-dki_param-md_dwimap.nii.gz
               <source_entities>_model-dki_param-mk_dwimap.json
               <source_entities>_model-dki_param-mk_dwimap.nii.gz
               <source_entities>_model-dki_param-mkt_dwimap.json
               <source_entities>_model-dki_param-mkt_dwimap.nii.gz
               <source_entities>_model-dki_param-rd_dwimap.json
               <source_entities>_model-dki_param-rd_dwimap.nii.gz
               <source_entities>_model-dki_param-rk_dwimap.json
               <source_entities>_model-dki_param-rk_dwimap.nii.gz
               <source_entities>_model-tensor_param-fa_dwimap.json
               <source_entities>_model-tensor_param-fa_dwimap.nii.gz
               # Microstructural metrics calculated if wmti is True
               <source_entities>_model-dkimicro_param-awf_dwimap.json
               <source_entities>_model-dkimicro_param-awf_dwimap.nii.gz
               <source_entities>_model-dkimicro_param-rde_dwimap.json
               <source_entities>_model-dkimicro_param-rde_dwimap.nii.gz

      qsirecon-TORTOISE/
         dataset_description.json
         sub-<label>[_ses-<label>].html
         logs/
         sub-<label>/[ses-<label>/]
            figures/
            dwi/
               <source_entities>_model-mapmri_param-ng_dwimap.json
               <source_entities>_model-mapmri_param-ng_dwimap.nii.gz
               <source_entities>_model-mapmri_param-ngpar_dwimap.json
               <source_entities>_model-mapmri_param-ngpar_dwimap.nii.gz
               <source_entities>_model-mapmri_param-ngperp_dwimap.json
               <source_entities>_model-mapmri_param-ngperp_dwimap.nii.gz
               <source_entities>_model-mapmri_param-pa_dwimap.json
               <source_entities>_model-mapmri_param-pa_dwimap.nii.gz
               <source_entities>_model-mapmri_param-path_dwimap.json
               <source_entities>_model-mapmri_param-path_dwimap.nii.gz
               <source_entities>_model-mapmri_param-rtap_dwimap.json
               <source_entities>_model-mapmri_param-rtap_dwimap.nii.gz
               <source_entities>_model-mapmri_param-rtop_dwimap.json
               <source_entities>_model-mapmri_param-rtop_dwimap.nii.gz
               <source_entities>_model-mapmri_param-rtpp_dwimap.json
               <source_entities>_model-mapmri_param-rtpp_dwimap.nii.gz
               <source_entities>_model-tensor_param-ad_dwimap.json
               <source_entities>_model-tensor_param-ad_dwimap.nii.gz
               <source_entities>_model-tensor_param-am_dwimap.json
               <source_entities>_model-tensor_param-am_dwimap.nii.gz
               <source_entities>_model-tensor_param-fa_dwimap.json
               <source_entities>_model-tensor_param-fa_dwimap.nii.gz
               <source_entities>_model-tensor_param-li_dwimap.json
               <source_entities>_model-tensor_param-li_dwimap.nii.gz
               <source_entities>_model-tensor_param-rd_dwimap.json
               <source_entities>_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 Atlases for more information on this output directory.