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README.md

Freesurfer recon-all BIDS App

Description

This app implements surface reconstruction using Freesurfer. It reconstructs the surface for each subject individually and then creates a study specific template. In case there are multiple sessions the Freesurfer longitudinal pipeline is used (creating subject specific templates) unless instructed to combine data across sessions.

The current Freesurfer version is based on: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz

The output of the pipeline consist of the SUBJECTS_DIR created during the analysis.

Documentation

How to report errors

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

Acknowledgements

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

Usage

This App has the following command line arguments:

    $ docker run -ti --rm bids/freesurfer --help
    usage: run.py [-h]
                  [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                  [--session_label SESSION_LABEL [SESSION_LABEL ...]]
                  [--n_cpus N_CPUS]
                  [--stages {autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all}
                            [{autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all} ...]]
                  [--steps {cross-sectional,template,longitudinal}
                           [{cross-sectional,template,longitudinal} ...]]
                  [--template_name TEMPLATE_NAME] --license_file LICENSE_FILE
                  [--acquisition_label ACQUISITION_LABEL]
                  [--refine_pial_acquisition_label REFINE_PIAL_ACQUISITION_LABEL]
                  [--multiple_sessions {longitudinal,multiday}]
                  [--refine_pial {T2,FLAIR,None,T1only}]
                  [--hires_mode {auto,enable,disable}]
                  [--parcellations {aparc,aparc.a2009s} [{aparc,aparc.a2009s} ...]]
                  [--measurements {area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind}
                                  [{area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind} ...]]
                  [-v] [--bids_validator_config BIDS_VALIDATOR_CONFIG]
                  [--skip_bids_validator] [--3T {true,false}]
                  bids_dir output_dir {participant,group1,group2}

    FreeSurfer recon-all + custom template generation.

    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. Multiple
                            participant level analyses can be run independently
                            (in parallel) using the same output_dir. "group1"
                            creates study specific group template. "group2"
                            exports group stats tables for cortical parcellation,
                            subcortical segmentation a table with euler numbers.

    optional arguments:
      -h, --help            show this help message and exit
      --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                            The label of the participant that should be analyzed.
                            The label corresponds to sub-<participant_label> 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.
      --session_label SESSION_LABEL [SESSION_LABEL ...]
                            The label of the session that should be analyzed. The
                            label corresponds to ses-<session_label> 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.
      --n_cpus N_CPUS       Number of CPUs/cores available to use.
      --stages {autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all}
                            [{autorecon1,autorecon2,autorecon2-cp,autorecon2-wm,autorecon-pial,autorecon3,autorecon-all,all} ...]
                            Autorecon stages to run.
      --steps {cross-sectional,template,longitudinal} [{cross-sectional,template,longitudinal} ...]
                            Longitudinal pipeline steps to run.
      --template_name TEMPLATE_NAME
                            Name for the custom group level template generated for
                            this dataset
      --license_file LICENSE_FILE
                            Path to FreeSurfer license key file. To obtain it you
                            need to register (for free) at
                            https://surfer.nmr.mgh.harvard.edu/registration.html
      --acquisition_label ACQUISITION_LABEL
                            If the dataset contains multiple T1 weighted images
                            from different acquisitions which one should be used?
                            Corresponds to "acq-<acquisition_label>"
      --refine_pial_acquisition_label REFINE_PIAL_ACQUISITION_LABEL
                            If the dataset contains multiple T2 or FLAIR weighted
                            images from different acquisitions which one should be
                            used? Corresponds to "acq-<acquisition_label>"
      --multiple_sessions {longitudinal,multiday}
                            For datasets with multiday sessions where you do not
                            want to use the longitudinal pipeline, i.e., sessions
                            were back-to-back, set this to multiday, otherwise
                            sessions with T1w data will be considered independent
                            sessions for longitudinal analysis.
      --refine_pial {T2,FLAIR,None,T1only}
                            If the dataset contains 3D T2 or T2 FLAIR weighted
                            images (~1x1x1), these can be used to refine the pial
                            surface. If you want to ignore these, specify None or
                            T1only to base surfaces on the T1 alone.
      --hires_mode {auto,enable,disable}
                            Submilimiter (high resolution) processing. 'auto' -
                            use only if <1.0mm data detected, 'enable' - force on,
                            'disable' - force off
      --parcellations {aparc,aparc.a2009s} [{aparc,aparc.a2009s} ...]
                            Group2 option: cortical parcellation(s) to extract
                            stats from.
      --measurements {area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind}
                            [{area,volume,thickness,thicknessstd,meancurv,gauscurv,foldind,curvind} ...]
                            Group2 option: cortical measurements to extract stats
                            for.
      -v, --version         show program's version number and exit
      --bids_validator_config BIDS_VALIDATOR_CONFIG
                            JSON file specifying configuration of bids-validator:
                            See https://github.com/INCF/bids-validator for more
                            info
      --skip_bids_validator
                            skips bids validation
  --3T {true,false}     enables the two 3T specific options that recon-all
  			supports: nu intensity correction params, and the 
			special schwartz atlas

Participant level

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

	docker run -ti --rm \
	-v /Users/filo/data/ds005:/bids_dataset:ro \
	-v /Users/filo/outputs:/outputs \
	-v /Users/filo/freesurfer_license.txt:/license.txt \
	bids/freesurfer \
	/bids_dataset /outputs participant --participant_label 01 \
	--license_file "/license.txt"

Group level

After doing this for all subjects (potentially in parallel) the group level analyses can be run.

Template creation

To create a study specific template run:

	docker run -ti --rm \
	-v /Users/filo/data/ds005:/bids_dataset:ro \
	-v /Users/filo/outputs:/outputs \
	-v /Users/filo/freesurfer_license.txt:/license.txt \
	bids/freesurfer \
	/bids_dataset /outputs group1 \
	--license_file "/license.txt"
Stats and quality tables export

To export tables with aggregated measurements within regions of cortical parcellation and subcortical segementation, and a table with euler numbers (a quality metric, see Rosen et. al, 2017) run:

	docker run -ti --rm \
	-v /Users/filo/data/ds005:/bids_dataset:ro \
	-v /Users/filo/outputs:/outputs \
	-v /Users/filo/freesurfer_license.txt:/license.txt \
	bids/freesurfer \
	/bids_dataset /outputs group2 \
	--license_file "/license.txt"

Also see the --parcellations and --measurements arguments.

This step writes ouput into <output_dir>/00_group2_stats_tables/. E.g.:

  • lh.aparc.thickness.tsv contains cortical thickness values for the left hemisphere extracted via the aparac parcellation.
  • aseg.tsv contains subcortical information from the aseg segmentation.
  • euler.tsv contains the euler numbers