Output Files

After running the workflow, the /path/to/output/dir folder will contain a hidden .logs folder for troubleshooting, as well as additional folders associated with the tools that were used to generate files (e.g. freesurfer, labelmerge), but for most purposes, all the primary outputs of interest will be in the mrtrix directory with the following structure:

mrtrix/
└── sub-{subject}
    ├── dti
    ├── dwi
    ├── response
    └── tractography

Briefly, dti contains processed diffusion tensor images along with quantitative maps (e.g. FA, MD, etc.), dwi contains images that were converted from Nifti (.nii.gz) to the MRtrix imaging format (.mif), response contains subject-specific response functions, and tractography contains tractogram files.

dti

This folder contains processed diffusion tensor images (DTI) that were used to compute quantitative maps (stored in the MRtrix imaging format - .mif), also found within the folder:

sub-{subject}
└── dti
    ├── sub-{subject}_model-dti_ad.mif
    ├── sub-{subject}_model-dti_fa.mif
    ├── sub-{subject}_model-dti_md.mif
    ├── sub-{subject}_model-dti_rd.mif
    └── sub-{subject}_model-dti_tensor.mif

As per the BIDS extension proposal, model-dti denotes to the DTI model used to process the data, and the suffix (ad, fa, md, rd, tensor) describes the imaging data.

dwi

This folder contains the input diffusion weighted image (dwi) and brain mask converted from Nifti (.nii.gz) to the MRtrix imaging format (.mif) used in downstream processing. It also contains an intensity normalized dwi image used for DTI:

sub-{subject}
└── dwi
    ├── sub-{subject}_desc-brain_mask.mif
    ├── sub-{subject}_desc-normalized_dwi.mif
    └── sub-{subject}_dwi.mif

response

This folder contains the subject-specific response functions that were estimated from the input diffusion data, as well as both the normalized and unnormalized versions of the estimated fibre orientation distribution (FOD) maps. Both response functions and FOD maps are estimated for the three different tissue types: white matter (wm), grey matter (gm), and corticospinal fluid (csf):

sub-{subject}
└── response
    ├── sub-{subject}_desc-csf_model-csd_fod.mif
    ├── sub-{subject}_desc-csf_model-csd_fodNormalized.mif
    ├── sub-{subject}_desc-csf_response.txt
    ├── sub-{subject}_desc-gm_model-csd_fod.mif
    ├── sub-{subject}_desc-gm_model-csd_fodNormalized.mif
    ├── sub-{subject}_desc-gm_response.txt
    ├── sub-{subject}_desc-wm_model-csd_fod.mif
    ├── sub-{subject}_desc-wm_model-csd_fodNormalized.mif
    └── sub-{subject}_desc-wm_response.txt

tractography

This folder contains generated tractogram data and associated files describing how streamlines connect different subcortical structures:

sub-{subject}
└── tractography
    ├── sub-{subject}_desc-filteredsubcortical_nodeAssignment.txt
    ├── sub-{subject}_desc-filteredsubcortical_nodeWeights.csv
    ├── sub-{subject}_desc-filteredsubcortical_tractography.tck
    ├── sub-{subject}_desc-iFOD2_muCoefficient
    ├── sub-{subject}_desc-iFOD2_tckWeights.txt
    ├── sub-{subject}_desc-iFOD2_tractography.tck
    ├── sub-{subject}_desc-subcortical_nodeAssignment.txt
    ├── sub-{subject}_desc-subcortical_nodeWeights.csv

The desc-filteredsubcortical entity pair describes associated tractogram files that have been filtered to only pass through WM and connect two GM structures, while the desc-subcortical entity pair denotes files associated with the unfiltered subcortical connectome. Whole-brain tractogram associated files are denoted by desc-iFOD2, which describes the tractography algorithm used to perform tractograpy.

Note: As the BIDS extension proposal has not been finalized, the naming of such files may be subject to change

Additional Files

The top-level /path/to/output/dir contains additional files / folders:

/path/to/output/dir
├── ...
├── config
├── .logs
├── .snakebids
└── .snakemake

The config folder, along with the hidden .snakebids and .snakemake folders contain a record of the code and parameters used, and paths to the inputs.

Workflow steps that write logs to file are stored in the hidden .logs subfolder, with the file names based on the tools used (e.g. mrtrix) and rule wildcards (e.g. subject).

If the app is run in workflow mode (--workflow-mode / -W), which enables direct use of the Snakemake CLI to run scattr, output folders (e.g. work) will be placed in a results folder.