BIDS-apps

Multi-echo combination

Before sharing or pre-processing their images, users may want to combine the separate the individual echos of multi-echo MRI acquisitions. The echcombine-tool is a wrapper around mecombine that writes BIDS valid output.

usage: echocombine [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-o OUTPUT]
                   [-a {PAID,TE,average}] [-w [WEIGHTS ...]] [-f]
                   bidsfolder pattern

A wrapper around the 'mecombine' multi-echo combination tool
(https://github.com/Donders-Institute/multiecho).

Except for BIDS inheritances, this wrapper is BIDS-aware (a 'bidsapp') and writes BIDS
compliant output

positional arguments:
  bidsfolder            The bids-directory with the (multi-echo) subject data
  pattern               Globlike recursive search pattern (relative to the subject/session folder) to
                        select the first echo of the images that need to be combined, e.g.
                        '*task-*echo-1*'

options:
  -h, --help            show this help message and exit
  -p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        Space separated list of sub-# identifiers to be processed (the sub-prefix can
                        be left out). If not specified then all sub-folders in the bidsfolder will be
                        processed (default: None)
  -o OUTPUT, --output OUTPUT
                        A string that determines where the output is saved. It can be the name of a
                        BIDS datatype folder, such as 'func', or of the derivatives folder, i.e.
                        'derivatives'. If output = [the name of the input datatype folder] then the
                        original echo images are replaced by one combined image. If output is left
                        empty then the combined image is saved in the input datatype folder and the
                        original echo images are moved to the 'extra_data' folder (default: )
  -a {PAID,TE,average}, --algorithm {PAID,TE,average}
                        Combination algorithm (default: TE)
  -w [WEIGHTS ...], --weights [WEIGHTS ...]
                        Weights for each echo (default: None)
  -f, --force           Process all images, regardless whether target images already exist. Otherwise
                        the echo-combination will be skipped (default: False)

examples:
  echocombine myproject/bids func/*task-stroop*echo-1*
  echocombine myproject/bids *task-stroop*echo-1* -p 001 003
  echocombine myproject/bids func/*task-*echo-1* -o func
  echocombine myproject/bids func/*task-*echo-1* -o derivatives -w 13 26 39 52
  echocombine myproject/bids func/*task-*echo-1* -a PAID

Defacing

Before sharing or pre-processing their images, users may want to deface their anatomical MRI acquisitions to protect the privacy of their subjects. The deface-tool is a wrapper around pydeface that writes BIDS valid output. NB: pydeface requires FSL to be installed on the system.

usage: deface [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-o OUTPUT] [-c] [-n NATIVESPEC]
              [-a ARGS] [-f]
              bidsfolder pattern

A wrapper around the 'pydeface' defacing tool (https://github.com/poldracklab/pydeface). Pydeface
requires an existing installation of FSL flirt

Except for BIDS inheritances and IntendedFor usage, this wrapper is BIDS-aware (a 'bidsapp')
and writes BIDS compliant output

Linux users can distribute the computations to their HPC compute cluster if the DRMAA
libraries are installed and the DRMAA_LIBRARY_PATH environment variable set

For multi-echo data see `medeface`

positional arguments:
  bidsfolder            The bids-directory with the subject data
  pattern               Globlike search pattern (relative to the subject/session folder) to select
                        the images that need to be defaced, e.g. 'anat/*_T1w*'

options:
  -h, --help            show this help message and exit
  -p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        Space separated list of sub-# identifiers to be processed (the sub-prefix can
                        be left out). If not specified then all sub-folders in the bidsfolder will be
                        processed (default: None)
  -o OUTPUT, --output OUTPUT
                        A string that determines where the defaced images are saved. It can be the
                        name of a BIDS datatype folder, such as 'anat', or of the derivatives folder,
                        i.e. 'derivatives'. If output is left empty then the original images are
                        replaced by the defaced images (default: None)
  -c, --cluster         Use the DRMAA library to submit the deface jobs to a high-performance compute
                        (HPC) cluster (default: False)
  -n NATIVESPEC, --nativespec NATIVESPEC
                        Opaque DRMAA argument with native specifications for submitting deface jobs
                        to the HPC cluster (NB: Use quotes and include at least one space character
                        to prevent premature parsing) (default: -l walltime=00:30:00,mem=2gb)
  -a ARGS, --args ARGS  Additional arguments (in dict/json-style) that are passed to pydeface (NB:
                        Use quotes). See examples for usage (default: {})
  -f, --force           Deface all images, regardless if they have already been defaced (i.e. if
                        {"Defaced": True} in the json sidecar file) (default: False)

examples:
  deface myproject/bids anat/*_T1w*
  deface myproject/bids anat/*_T1w* -p 001 003 -o derivatives
  deface myproject/bids anat/*_T1w* -c -n "-l walltime=00:60:00,mem=4gb"
  deface myproject/bids anat/*_T1w* -a '{"cost": "corratio", "verbose": ""}'

Multi-echo defacing

This utility is very similar to the deface utility above, except that it can handle multi-echo data.

usage: medeface [-h] [-m MASKPATTERN] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-o OUTPUT] [-c]
                [-n NATIVESPEC] [-a ARGS] [-f]
                bidsfolder pattern

A wrapper around the 'pydeface' defacing tool (https://github.com/poldracklab/pydeface) that
computes a defacing mask on a (temporary) echo-combined image and then applies it to each
individual echo-image. Pydeface requires an existing installation of FSL flirt

Except for BIDS inheritances and IntendedFor usage, this wrapper is BIDS-aware (a 'bidsapp')
and writes BIDS compliant output

Linux users can distribute the computations to their HPC compute cluster if the DRMAA
libraries are installed and the DRMAA_LIBRARY_PATH environment variable set

For single-echo data see `deface`

positional arguments:
  bidsfolder            The bids-directory with the (multi-echo) subject data
  pattern               Globlike search pattern (relative to the subject/session folder) to select
                        the images that need to be defaced, e.g. 'anat/*_T2starw*'

options:
  -h, --help            show this help message and exit
  -m MASKPATTERN, --maskpattern MASKPATTERN
                        Globlike search pattern (relative to the subject/session folder) to select
                        the images from which the defacemask is computed, e.g. 'anat/*_part-
                        mag_*_T2starw*'. If not given then 'pattern' is used (default: None)
  -p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        Space separated list of sub-# identifiers to be processed (the sub-prefix can
                        be left out). If not specified then all sub-folders in the bidsfolder will be
                        processed (default: None)
  -o OUTPUT, --output OUTPUT
                        A string that determines where the defaced images are saved. It can be the
                        name of a BIDS datatype folder, such as 'anat', or of the derivatives folder,
                        i.e. 'derivatives'. If output is left empty then the original images are
                        replaced by the defaced images (default: None)
  -c, --cluster         Use the DRMAA library to submit the deface jobs to a high-performance compute
                        (HPC) cluster (default: False)
  -n NATIVESPEC, --nativespec NATIVESPEC
                        Opaque DRMAA argument with native specifications for submitting deface jobs
                        to the HPC cluster (NB: Use quotes and include at least one space character
                        to prevent premature parsing) (default: -l walltime=00:30:00,mem=2gb)
  -a ARGS, --args ARGS  Additional arguments (in dict/json-style) that are passed to pydeface (NB:
                        Use quotes). See examples for usage (default: {})
  -f, --force           Process all images, regardless if images have already been defaced (i.e. if
                        {"Defaced": True} in the json sidecar file) (default: False)

examples:
  medeface myproject/bids anat/*_T1w*
  medeface myproject/bids anat/*_T1w* -p 001 003 -o derivatives
  medeface myproject/bids anat/*_T1w* -c -n "-l walltime=00:60:00,mem=4gb"
  medeface myproject/bids anat/*acq-GRE* -m anat/*acq-GRE*magnitude*"
  medeface myproject/bids anat/*_FLAIR* -a '{"cost": "corratio", "verbose": ""}'

Skull-stripping

The skullstrip-tool is a wrapper around the synthstrip tool that writes BIDS valid output

usage: skullstrip [-h] [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-m MASKED]
                  [-o OUTPUT [OUTPUT ...]] [-f] [-a ARGS] [-c] [-n NATIVESPEC]
                  bidsfolder pattern

A wrapper around FreeSurfer's 'synthstrip' skull stripping tool
(https://surfer.nmr.mgh.harvard.edu/docs/synthstrip). Except for BIDS inheritances,
this wrapper is BIDS-aware (a 'bidsapp') and writes BIDS compliant output

The corresponding brain mask is saved in the bids/derivatives/synthstrip folder

Assumes the installation of FreeSurfer v7.3.2 or higher

positional arguments:
  bidsfolder            The bids-directory with the subject data
  pattern               Globlike search pattern (relative to the subject/session folder) to select
                        the (3D) images that need to be skullstripped, e.g. 'anat/*_T1w*'

options:
  -h, --help            show this help message and exit
  -p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        Space separated list of sub-# identifiers to be processed (the sub-prefix can
                        be left out). If not specified then all sub-folders in the bidsfolder will be
                        processed (default: None)
  -m MASKED, --masked MASKED
                        Globlike search pattern (relative to the subject/session folder) to select
                        additional (3D/4D) images from the same space that need to be masked with the
                        same mask, e.g. 'fmap/*_phasediff'. NB: This option can only be used if
                        pattern yields a single file per session (default: None)
  -o OUTPUT [OUTPUT ...], --output OUTPUT [OUTPUT ...]
                        One or two output strings that determine where the skullstripped + additional
                        masked images are saved. Each output string can be the name of a BIDS
                        datatype folder, such as 'anat', or of the derivatives folder, i.e.
                        'derivatives' (default). If the output string is the same as the datatype
                        then the original images are replaced by the skullstripped images (default:
                        None)
  -f, --force           Process images, regardless whether images have already been skullstripped
                        (i.e. if {'SkullStripped': True} in the json sidecar file) (default: False)
  -a ARGS, --args ARGS  Additional arguments that are passed to synthstrip (NB: Use quotes and
                        include at least one space character to prevent premature parsing) (default:)
  -c, --cluster         Use the DRMAA library to submit the skullstrip jobs to a high-performance
                        compute (HPC) cluster (default: False)
  -n NATIVESPEC, --nativespec NATIVESPEC
                        Opaque DRMAA argument with native specifications for submitting skullstrip
                        jobs to the HPC cluster (NB: Use quotes and include at least one space
                        character to prevent premature parsing) (default: -l walltime=0:05:00,mem=8gb)

examples:
  skullstrip myproject/bids anat/*_T1w*
  skullstrip myproject/bids anat/*_T1w* -p 001 003 -a " --no-csf"
  skullstrip myproject/bids fmap/*_magnitude1* -m fmap/*_phasediff* -o extra_data fmap
  skullstrip myproject/bids fmap/*_acq-mylabel*_magnitude1* -m fmap/*_acq-mylabel_* -o fmap

Quality control

Slicereport is a very flexible QC report generator for doing visual inspections on your BIDS data.

usage: slicereport [-h] [-o OUTLINEPATTERN] [-i OUTLINEIMAGE]
                   [-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-r REPORTFOLDER]
                   [-x XLINKFOLDER [XLINKFOLDER ...]] [-q QCSCORES [QCSCORES ...]]
                   [-c {torque,slurm}] [-m MEM] [--operations OPERATIONS]
                   [--suboperations SUBOPERATIONS] [--options OPTIONS [OPTIONS ...]]
                   [--outputs OUTPUTS [OUTPUTS ...]] [--suboptions SUBOPTIONS [SUBOPTIONS ...]]
                   [--suboutputs SUBOUTPUTS [SUBOUTPUTS ...]]
                   bidsfolder pattern

A wrapper around the 'fslmaths' (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils) and 'slicer'
imaging tools (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Miscvis) to generate a web page with a
row of image slices for each subject in the BIDS repository, as well as individual sub-pages
displaying more detailed information. The input images are selectable using wildcards (all
nibabel image formats are supported), and the output images are configurable via various user
options, allowing you to quickly create a custom 'slicer' report to do visual quality control
on any 3D/4D imagetype in your repository.

Requires an existing installation of FSL tools (i.e. fsl-libvis, fsl-avwutils and fsl-flirt)

Set the environment variable BIDSCOIN_DEBUG=TRUE to save intermediate data

positional arguments:
  bidsfolder            The bids-directory with the subject data
  pattern               Globlike search pattern to select the images in bidsfolder to be reported,
                        e.g. 'anat/*_T2starw*'

options:
  -h, --help            show this help message and exit
  -o OUTLINEPATTERN, --outlinepattern OUTLINEPATTERN
                        Globlike search pattern to select red outline images that are projected on
                        top of the reported images (i.e. 'outlinepattern' must yield the same number
                        of images as 'pattern'. Prepend `outlinedir:` if your outline images are in
                        `outlinedir` instead of `bidsdir` (see examples below)`
  -i OUTLINEIMAGE, --outlineimage OUTLINEIMAGE
                        A common red-outline image that is projected on top of all images
  -p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        Space separated list of sub-# identifiers to be processed (the sub-prefix can
                        be left out). If not specified then all sub-folders in the bidsfolder will be
                        processed
  -r REPORTFOLDER, --reportfolder REPORTFOLDER
                        The folder where the report is saved (default:
                        bidsfolder/derivatives/slicereport)
  -x XLINKFOLDER [XLINKFOLDER ...], --xlinkfolder XLINKFOLDER [XLINKFOLDER ...]
                        A (list of) QC report folder(s) with cross-linkable sub-reports, e.g.
                        bidsfolder/derivatives/mriqc
  -q QCSCORES [QCSCORES ...], --qcscores QCSCORES [QCSCORES ...]
                        Column names for creating an accompanying tsv-file to store QC-rating scores
                        (default: rating_overall)
  -c {torque,slurm}, --cluster {torque,slurm}
                        Use `torque` or `slurm` to submit the slicereport jobs to a high-performance
                        compute (HPC) cluster
  -m MEM, --mem MEM     The amount of requested memory in GB for the cluster jobs
  --operations OPERATIONS
                        One or more fslmaths operations that are performed on the input image (before
                        slicing it for the report). OPERATIONS is opaquely passed as is: `fslmaths
                        inputimage OPERATIONS reportimage`. NB: Use quotes and include at least one
                        space character to prevent premature parsing, e.g. " -Tmean" or "-Tstd -s 3"
                        (default: -Tmean)
  --suboperations SUBOPERATIONS
                        The same as OPERATIONS but then for the sub-report instead of the main
                        report: `fslmaths inputimage SUBOPERATIONS subreportimage` (default: -Tmean)
  --options OPTIONS [OPTIONS ...]
                        Main options of slicer (see below). (default: "s 1")
  --outputs OUTPUTS [OUTPUTS ...]
                        Output options of slicer (see below). (default: "x 0.4 x 0.5 x 0.6 y 0.4 y
                        0.5 y 0.6 z 0.4 z 0.5 z 0.6")
  --suboptions SUBOPTIONS [SUBOPTIONS ...]
                        Main options of slicer for creating the sub-reports (same as OPTIONS, see
                        below). (default: OPTIONS)
  --suboutputs SUBOUTPUTS [SUBOUTPUTS ...]
                        Output options of slicer for creating the sub-reports (same as OUTPUTS, see
                        below). (default: "S 4 1600")

OPTIONS:
  L                  : Label slices with slice number.
  l [LUT]            : Use a different colour map from that specified in the header (see $FSLDIR/etc/luts)
  i [MIN] [MAX]      : Specify intensity min and max for display range.
  e [THR]            : Use the specified threshold for edges (if > 0 use this proportion of max-min,
                       if < 0, use the absolute value)
  t                  : Produce semi-transparent (dithered) edges.
  n                  : Use nearest-neighbour interpolation for output.
  u                  : Do not put left-right labels in output.
  s                  : Size scaling factor
  c                  : Add a red dot marker to top right of image

OUTPUTS:
  x/y/z [SLICE] [..] : Output sagittal, coronal or axial slice (if SLICE > 0 it is a fraction of
                       image dimension, if < 0, it is an absolute slice number)
  a                  : Output mid-sagittal, -coronal and -axial slices into one image
  A [WIDTH]          : Output _all_ axial slices into one image of _max_ width WIDTH
  S [SAMPLE] [WIDTH] : As `A` but only include every SAMPLE'th slice
  LF                 : Start a new line (i.e. works like a row break)

examples:
  slicereport bids anat/*_T1w*
  slicereport bids anat/*_T2w* -r QC/slicereport_T2 -x QC/slicereport_T1
  slicereport bids fmap/*_phasediff* -o fmap/*_magnitude1*
  slicereport bids/derivatives/fmriprep func/*desc-preproc_bold* --suboperations " -Tstd"
  slicereport bids/derivatives/fmriprep anat/*desc-preproc_T1w* -o anat/*label-GM* -x bids/derivatives/fmriprep
  slicereport bids/derivatives/deface anat/*_T1w* -o bids:anat/*_T1w* --options L e 0.05
  slicereport bids anat/*_T1w* --outputs x 0.3 x 0.4 x 0.5 x 0.6 x 0.7 LF z 0.3 z 0.4 z 0.5 z 0.6 z 0.7
_images/slicereport_skullstrip.png

Snippet of a slicereport for doing quality control on skullstrip output images (see above). The background image shows the skull-stripped image in the extra_data folder, and the red outline image on top shows the contours of the original image in the anat folder. Users can click on an image to navigate to the individual (more detailed) slicereport of that subject. This example can be generated from scratch with just two commands:

$ skullstrip bids anat/*run-1_T1w* -o extra_data
$ slicereport bids extra_data/*run-1_T1w* -o anat/*run-1_T1w*

Click here to view a sample slicereport