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https://github.com/bids-apps/tracula

implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.
https://github.com/bids-apps/tracula

bids bidsapp diffusion-mri

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implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session) input data.

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README 

        
# TRACULA BIDS App



[![CircleCI](https://circleci.com/gh/BIDS-Apps/tracula.svg?style=shield&circle-token=:circle-token)](https://circleci.com/gh/BIDS-Apps/tracula)

[![DOI](https://zenodo.org/badge/77473131.svg)](https://zenodo.org/badge/latestdoi/77473131)



## Description



This [BIDS App](https://bids-apps.neuroimaging.io) implements

[Freesurfer's](https://surfer.nmr.mgh.harvard.edu/)

[TRACULA ](https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula)

(TRActs Constrained by UnderLying Anatomy) tool for

cross-sectional as well as longitudinal (multi session) input data.



This tool is based on Freesurfer v6.0.0



## Disclaimer



This BIDS-App was tested with [high-angular resolution

diffusion weighted imaging (DWI) data without

fieldmaps](https://openfmri.org/dataset/ds000114/).

If you would like to see it working with more complex data,

[get in touch](https://github.com/bids-apps/tracula/issues).



## How to report errors



For Tracula-BIDS-Apps related problems, open an

[issue](https://github.com/bids-apps/tracula/issues).



For Tracula-relade errors contact the

[Freesurfer mailing list](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport).



## Acknowledgements



If you use this tool please cite the following sources:



- *Franziskus Liem, & Krzysztof J. Gorgolewski. (2017).

BIDS-Apps/tracula.* [![DOI](https://zenodo.org/badge/77473131.svg)](https://zenodo.org/badge/latestdoi/77473131)



- The BIDS Apps

[preprint](http://biorxiv.org/content/early/2016/10/20/079145):

*Krzysztof J. Gorgolewski et al. (2017).

BIDS Apps: Improving ease of use, accessibility and reproducibility

of neuroimaging data analysis methods.

doi: https://doi.org/10.1101/079145*



- The relevant Freesurfer

[references](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation).



## Data



Tracula requires one DWI volume and a one T1w image

per participant (or session if the data is longitudinal).



In a first step, the app will run the FreeSurfer reconstruction

(`recon-all`). If the Freesurfer reconstruction is already available

and is provided via the `{freesurfer_dir}` argument, this step is skipped.

In this case `recon-all` should have been performed with the

[Freesurfer BIDS App](https://github.com/bids-apps/freesurfer)

(or at least follow the BIDS naming scheme).



## Analysis levels



- **participant**: Tract reconstruction



    Runs `recon-all` if not already available.

    Subsequently, performs the three steps (prep, bedp, path) of Tracula's `trac-all`,

    reconstructing major fiber tracts form Freesurfer outputs and

    DWI raw data.

    All data is written into `{output_dir}`.



- **group1**: Motion statistics



    Collects motion statistics for multiple subjects into one file.

    Additionally, total motion index (TMI, according to

    [Yendiki et al., 2013](http://doi.org/10.1016/j.neuroimage.2013.11.027)).

    Output is written to

    `{output_dir}/00_group1_motion_stats/group_motion.tsv`.



    *Note*: In deviation to the original equation

    (which includes rotation, translation, bad slices, dropout score),

    this implementation of TMI only considers those measures

    that show enought variance for normalization (i.e., don't

    produce NaNs - often seen in 'PercentBadSlices' and

    'AvgDropoutScore'). The measures that went into the

    calculation can be found in the *TMI_info* column of the

    output file.



- **group2**: Tract statistics



    Collects tract stats for multiple subjects.

    Mean stats of a tract (average FA...) are written to

    `{output_dir}/00_group2_tract_stats/overall_stats/`.

    Along-tract stats are written to

    `{output_dir}/00_group2_tract_stats/byvoxel_stats/`.



## Usage



This App has the following command line arguments:



    usage: run.py [-h] --license_key LICENSE_KEY

                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]

                  [--session_label SESSION_LABEL [SESSION_LABEL ...]]

                  [--freesurfer_dir FREESURFER_DIR]

                  [--stages {prep,bedp,path,all} [{prep,bedp,path,all} ...]]

                  [--n_cpus N_CPUS] [--run-freesurfer-tests-only] [-v]

                  bids_dir output_dir {participant,group1,group2}



    BIDS App for Tracula processing stream.

    https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula



    positional arguments:

      bids_dir              The directory with the input dataset formatted

                            according to the BIDS standard.

      output_dir            The directory where the output files should be stored.

                            If you are running group level analysis this folder

                            should be prepopulated with the results of

                            theparticipant level analysis.

      {participant,group1,group2}

                            Level of the analysis that will be performed.

                            "participant": runs FreeSurfer and reconstructs paths

                            (trac-all -prep, -bedp and -path), "group1": collects

                            motion stats in one file, "group2": collects tract

                            stats in one file.



    optional arguments:

      -h, --help            show this help message and exit

      --license_key LICENSE_KEY

                            FreeSurfer license key - letters and numbers after "*"

                            in the email you received after registration. To

                            register (for free) visit

                            https://surfer.nmr.mgh.harvard.edu/registration.html

                            (default: None)

      --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]

                            The label of the participant that should be analyzed.

                            The label corresponds to sub- from

                            the BIDS spec (so it does not include "sub-"). If this

                            parameter is not provided all subjects should be

                            analyzed. Multiple participants can be specified with

                            a space separated list. (default: None)

      --session_label SESSION_LABEL [SESSION_LABEL ...]

                            The label of the sessions that should be analyzed. The

                            label corresponds to ses- from the BIDS

                            spec (so it does not include "ses-"). If this

                            parameter is not provided all sessions should be

                            analyzed. Multiple sessions can be specified with a

                            space separated list. (default: None)

      --freesurfer_dir FREESURFER_DIR

                            The directory with the FreeSurfer data. If not

                            specified, FreeSurfer data is written into output_dir.

                            If FreeSurfer data cannot be found for a subject, this

                            app will run FreeSurfer as well. (default: None)

      --stages {prep,bedp,path,all} [{prep,bedp,path,all} ...]

                            Participant-level trac-all stages to run. Passing"all"

                            will run "prep", "bedp" and "path". (default: ['all'])

      --n_cpus N_CPUS       Number of CPUs/cores available to use. (default: 1)

      --run-freesurfer-tests-only

                            Dev option to enable freesurfer tests on circleci

                            (default: False)

      -v, --version         show program's version number and exit



## Examples



To run it in participant level mode (for one participant):



### Participant level



        docker run -ti --rm \

         -v /data/ds114/sourcedata:/bids_dataset:ro \

         -v /data/ds114/derivates/tracula:/outputs \

         -v /data/ds114/derivates/freesurfer:/freesurfer \

         bids/tracula \

         /bids_dataset /outputs participant --participant_label 01 \

         --license_key "XXXXXXXX" \

         --freesurfer_dir /freesurfer



**Note that** the path specified in --freesurfer_dir needs to be the

mount point inside the docker container (e.g., `/freesurfer`, specified

in the 4th line of the previous command, after the ":"), not the

path on your hard drive (e.g., `/data/ds114/derivates/freesurfer`)



### Group level



After doing this for all subjects (potentially in parallel) the group level analysis

can be run.



To aggregate motion statistics into one file (group1 stage), run:



        docker run -ti --rm \

         -v /data/ds114/sourcedata:/bids_dataset:ro \

         -v /data/ds114/derivates/tracula:/outputs \

         -v /data/ds114/derivates/freesurfer:/freesurfer \

         bids/tracula \

         /bids_dataset /outputs group1 \

         --license_key "XXXXXXXX" \

         --freesurfer_dir /freesurfer



To aggregate tract statistics into one file  (group2 stage), run:



        docker run -ti --rm \

         -v /data/ds114/sourcedata:/bids_dataset:ro \

         -v /data/ds114/derivates/tracula:/outputs \

         -v /data/ds114/derivates/freesurfer:/freesurfer \

         bids/tracula \

         /bids_dataset /outputs group2 \

         --license_key "XXXXXXXX" \

         --freesurfer_dir /freesurfer