SLICEREPORT(1)

📦
version 4.6.2 · 2 versions
, in fedora 43

🎀 NAME 🎀

slicereport — bestie, it's the slice-report generator, and it's iconic 💅

✨ SYNOPSIS ✨

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

💖 DESCRIPTION 💖

Okay so picture this: slicereport is a wrapper around the fslmaths tool (<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils>) and the slicer imaging tool (<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Miscvis>), and what it does is generate a web page with a whole row of image slices for every single subject in your BIDS repository — plus individual sub-pages with even more detailed info. It's giving main character energy fr fr. 🌈

You pick your input images with wildcards (and yes, literally all nibabel image formats are supported, no cap), and the output images are configurable through a bunch of user options, so you can quickly build a custom slicer report to do visual quality control on any 3D/4D imagetype in your repository. Obsessed. 👑

Heads up bestie: this requires an existing installation of FSL tools (i.e. fsl-libvis, fsl-avwutils and fsl-flirt). No FSL, no report, sorry 😭
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 💅

  • -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, ngl that's a nice touch). 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") 🧚

🔥 COMMENTS 🔥

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

👑 AUTHOR 👑

Marcel Zwiers <m.zwiers@donders.ru.nl> — absolute legend, thank you for your service 🫡

And that's a wrap, bestie! This page came to you from the bidscoin fam, version 4.6.2, dated 2025-11-06 — the SLICEREPORT(1) era, no cap 💖✨ Slay, go make some beautiful slice reports. 💅🦋

📦 where this page comes from