Name

dmri_bids_config: Configure TRACULA to run on a BIDS-formatted dataset

Usage

dmri_bids_config --in <directory> -c <configfile>

This script will take as its input a BIDS-formatted study directory and output: 1. A TRACULA configuration file: This file is needed to pre-process the DWI data, reconstruct tracts of interest, etc. with trac-all. 2. A FreeSurfer Group Descriptor (FSGD) file: This file is needed to perform statistics on the output tract measures with mri_glmfit. It will be generated if the input BIDS directory contains a participants.tsv file.

After you run dmri_bids_config It is important that you inspect the configuration file to make sure that everything has been set up the way you intended.

Arguments

Required arguments

--in <directory>

Path to the input data (the top-level BIDS directory for the study, not a single subject or session directory)

At least one of the following two is required

--c <file>

Output configuration file that specifies DWI inputs and analysis options for TRACULA

--f <file>

Output FSGD file that specifies subject-specific continuous and discrete variables for linear regression analyses (default: append .fsgd to the argument of --c)

Optional arguments

--fsdir <directory>

FreeSurfer SUBJECTS_DIR for this study (must be specified, either here or with: setenv SUBJECTS_DIR ...)

--trdir <directory>

Output TRACULA directory for this study (If not specified, TRACULA will use the FreeSurfer SUBJECTS_DIR)

--acq <name>

Only use DWI scans collected with this acquisition (The name of the NIfTI volumes in BIDS must include the string acq- followed by this name)

See also

dmrirc, trac-all

Links

TRACULA

References

If you use TRACULA, please cite:
Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy. Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, Wang R, Salat D, Ehrlich S, Behrens T, Jbabdi S, Gollub R and Fischl B (2011). Front. Neuroinform. 5:23. doi: 10.3389/fninf.2011.00023
Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data. Maffei C, Lee C, Planich M, Ramprasad M, Ravi N, Trainor D, Urban Z, Kim M, Jones R, Henin A, Hofmann S, Pizzagalli D, Auerbach R, Gabrieli J, Whitfield-Gabrieli S, Greve D, Haber N, Yendiki A (2021). NeuroImage 245:118706.
If you use our measures of head motion, please cite:
Spurious group differences due to head motion in a diffusion MRI study. Yendiki A, Koldewyn K, Kakunoori S, Kanwisher N, Fischl B (2014). NeuroImage 88:79–90.
If you use the longitudinal stream of TRACULA, please cite:
Joint reconstruction of white-matter pathways from longitudinal diffusion MRI data with anatomical priors. Yendiki A, Reuter, M, Wilkens P, Rosas H D, Fischl B (2016). NeuroImage 127:277–286.

Reporting Bugs

Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >

Author/s

Anastasia Yendiki

-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-USAGE: dmri_bids_config
+'''Index''' <<TableOfContents>>
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-Required inputs

   --in <directory>:

     Path to the input data (the top-level BIDS directory, not a

     single subject or session directory)
+= Name =

dmri_bids_config: Configure [[Tracula|TRACULA]] to run on a [[https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html|BIDS]]-formatted dataset
-Line 8:
+Line 6:
-At least one of the following two is required

   --c <file>:

     Output TRACULA configuration file

   --f <file>:

     Output FSGD file (default: append .fsgd to argument of --c)
+= Usage =

{{{

dmri_bids_config --in <directory> -c <configfile>

}}}
-Line 14:
+Line 11:
-Optional inputs

   --fsdir <directory>:

     FreeSurfer SUBJECTS_DIR for this study

     (Must either specify here or with: setenv SUBJECTS_DIR ...)

   --trdir <directory>:

     Output TRACULA directory for this study

     (If not specified, TRACULA will use the FreeSurfer SUBJECTS_DIR)

   --acq <name>:

     Only use diffusion MRI scans collected with this acquisition

     (The name of the NIfTI volumes in BIDS must include the string

     acq- followed by this name)
+This script will take as its input a BIDS-formatted study directory and output:

1. A [[dmrirc|TRACULA configuration]] file: This file is needed to pre-process the DWI data, reconstruct tracts of interest, etc. with [[trac-all]].

2. A [[FsgdFormat|FreeSurfer Group Descriptor (FSGD)]] file: This file is needed to perform statistics on the output tract measures with [[mri_glmfit]]. It will be generated if the input BIDS directory contains a '''participants.tsv'' file.



'''After you run dmri_bids_config'''

It is important that you inspect the configuration file to make sure that everything has been set up the way you intended.



= Arguments =

== Required arguments ==

 ||--in&nbsp;<directory> || Path to the input data (the top-level BIDS directory for the study, not a single subject or session directory) ||



== At least one of the following two is required ==

 ||--c&nbsp;<file> || Output [[dmrirc|configuration file]] that specifies DWI inputs and analysis options for TRACULA ||

 ||--f&nbsp;<file> || Output [[FsgdFormat|FSGD file]] that specifies subject-specific continuous and discrete variables for linear regression analyses (default: append '''.fsgd''' to the argument of --c) ||



== Optional arguments ==

 ||--fsdir&nbsp;<directory> || FreeSurfer SUBJECTS_DIR for this study (must be specified, either here or with: '''setenv SUBJECTS_DIR ...''') ||

 ||--trdir&nbsp;<directory> || Output TRACULA directory for this study (If not specified, TRACULA will use the FreeSurfer SUBJECTS_DIR) ||

 ||--acq&nbsp;<name> || Only use DWI scans collected with this acquisition (The name of the NIfTI volumes in BIDS must include the string '''acq-''' followed by this name) ||



= See also =

[[dmrirc]], [[trac-all]]



= Links =

[[Tracula|TRACULA]]



= References =

If you use TRACULA, please cite:



 . [[http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract|Automated probabilistic reconstruction of white-matter pathways in health and disease using an atlas of the underlying anatomy.]] Yendiki A, Panneck P, Srinivasan P, Stevens A, Zöllei L, Augustinack J, Wang R, Salat D, Ehrlich S, Behrens T, Jbabdi S, Gollub R and Fischl B (2011). ''Front. Neuroinform.'' 5:23. doi: 10.3389/fninf.2011.00023

 . [[https://www.sciencedirect.com/science/article/pii/S1053811921009782|Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data.]] Maffei C, Lee C, Planich M, Ramprasad M, Ravi N, Trainor D, Urban Z, Kim M, Jones R, Henin A, Hofmann S, Pizzagalli D, Auerbach R, Gabrieli J, Whitfield-Gabrieli S, Greve D, Haber N, Yendiki A (2021). ''!NeuroImage'' 245:118706.



If you use our measures of head motion, please cite:



 . [[http://www.sciencedirect.com/science/article/pii/S1053811913011312|Spurious group differences due to head motion in a diffusion MRI study.]] Yendiki A, Koldewyn K, Kakunoori S, Kanwisher N, Fischl B (2014). ''!NeuroImage'' 88:79–90.



If you use the longitudinal stream of TRACULA, please cite:



 . [[http://www.sciencedirect.com/science/article/pii/S1053811915011167|Joint reconstruction of white-matter pathways from longitudinal diffusion MRI data with anatomical priors.]] Yendiki A, Reuter, M, Wilkens P, Rosas H D, Fischl B (2016). ''!NeuroImage'' 127:277–286.



= Reporting Bugs =

Report bugs to < analysis-bugs@nmr.mgh.harvard.edu >



= Author/s =

Anastasia Yendiki

--c <file>	Output configuration file that specifies DWI inputs and analysis options for TRACULA
--f <file>	Output FSGD file that specifies subject-specific continuous and discrete variables for linear regression analyses (default: append .fsgd to the argument of --c)

--fsdir <directory>	FreeSurfer SUBJECTS_DIR for this study (must be specified, either here or with: setenv SUBJECTS_DIR ...)
--trdir <directory>	Output TRACULA directory for this study (If not specified, TRACULA will use the FreeSurfer SUBJECTS_DIR)
--acq <name>	Only use DWI scans collected with this acquisition (The name of the NIfTI volumes in BIDS must include the string acq- followed by this name)