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*'
optional arguments:
-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 If this flag is given subjects will be processed, regardless of
existing target files 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).
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*'
optional arguments:
-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 Flag to use the DRMAA library to submit the deface jobs to a high-
performance compute (HPC) cluster (default: False)
-n NATIVESPEC, --nativespec NATIVESPEC
DRMAA native specifications for submitting deface jobs to the HPC
cluster (default: -l walltime=00:30:00,mem=2gb)
-a ARGS, --args ARGS Additional arguments (in dict/json-style) that are passed to
pydeface. See examples for usage (default: {})
-f, --force If this flag is given images will be processed, regardless if images
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.
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*'
optional arguments:
-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 Flag to submit the deface jobs to a high-performance compute (HPC)
cluster (default: False)
-n NATIVESPEC, --nativespec NATIVESPEC
DRMAA native specifications for submitting deface jobs to the HPC
cluster (default: -l walltime=00:30:00,mem=2gb)
-a ARGS, --args ARGS Additional arguments (in dict/json-style) that are passed to
pydeface. See examples for usage (default: {})
-f, --force If this flag is given images will be processed, 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]
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*'
optional arguments:
-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 a leading space to prevent unintended argument parsing)
-c, --cluster Use `qsub` to submit the skullstrip jobs to a high-performance compute
(HPC) cluster. Can only be used if `--masked` is left empty (default: False)
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.py [-h] [-o OUTLINEPATTERN] [-i OUTLINEIMAGE]
[-p PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-r REPORTFOLDER]
[-q QCSCORES [QCSCORES ...]] [-c] [--options OPTIONS [OPTIONS ...]]
[--outputs OUTPUTS [OUTPUTS ...]] [--suboptions SUBOPTIONS [SUBOPTIONS ...]]
[--suboutputs SUBOUTPUTS [SUBOUTPUTS ...]]
bidsfolder pattern
A wrapper around the 'slicer' imaging tool (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, 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
datatype in your repository.
Requires an existing installation of FSL/slicer
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, --cluster Use `qsub` to submit the slicer jobs to a high-performance compute (HPC) cluster
--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.
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 myproject/bids anat/*_T1w*
slicereport myproject/bids anat/*_T2w* -r myproject/QC/slicereport_T2 -x myproject/QC/slicereport_T1
slicereport myproject/bids fmap/*_phasediff* -o fmap/*_magnitude1*
slicereport myproject/bids/derivatives/fmriprep anat/*run-?_desc-preproc_T1w* -o anat/*run-?_label-GM*
slicereport myproject/bids/derivatives/deface anat/*_T1w* -o myproject/bids:anat/*_T1w* --options L e 0.05
slicereport myproject/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
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*