slicereport - Man Page

slicereport [-h] [-o PATTERN] [-i FILENAME] [-p LABEL [LABEL ...]] [-r FOLDER] [-x FOLDER [FOLDER ...]] [-q NAME [NAME ...]] [-c [SPECS]] [--operations OPERATIONS] [--suboperations OPERATIONS] [--options Options [Options ...]] [--outputs OUTPUTS [OUTPUTS ...]] [--suboptions Options [Options ...]] [--suboutputs OUTPUTS [OUTPUTS ...]] 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

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*'

-o PATTERN, --outlinepattern PATTERN

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 FILENAME, --outlineimage FILENAME

A common red-outline image that is projected on top of all images

-p LABEL [LABEL ...], --participant LABEL [LABEL ...]

Space separated list of sub-# identifiers to be processed (the sub-prefix can be left out). If not specified then all participants will be processed

-r FOLDER, --reportfolder FOLDER

The folder where the report is saved (default: bidsfolder/derivatives/slicereport)

-x FOLDER [FOLDER ...], --xlinkfolder FOLDER [FOLDER ...]

A (list of) QC report folder(s) with cross-linkable sub-reports, e.g. bidsfolder/derivatives/mriqc

-q NAME [NAME ...], --qcscores NAME [NAME ...]

Column names for creating an accompanying tsv-file to store QC-rating scores (default: rating_overall)

-c [SPECS], --cluster [SPECS]

Use the DRMAA library to submit the slicereport jobs to a high-performance compute (HPC) cluster. You can add an opaque DRMAA argument with native specifications for your HPC resource manager (NB: Use quotes and include at least one space character to prevent premature parsing -- see examples)

--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 OPERATIONS

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 OPTIONS [OPTIONS ...]

Main options of slicer for creating the sub-reports (same as OPTIONS, see below). (default: OPTIONS)

--suboutputs OUTPUTS [OUTPUTS ...]

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* -c "--time=00:10:00 --mem=2000"
 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

Marcel Zwiers <m.zwiers@donders.ru.nl>