NIPY_DIAGNOSE(1)

📦
version 0.6.1 · 2 versions
, in fedora 43

💖 NIPY_DIAGNOSE(1) 💖

okay bestie, welcome to the User Commands section of the manual, and lemme tell you, this one is a whole vibe. it's called nipy_diagnose, and it's here to do one thing and do it gorgeously. ✨

🌸 NAME 🌸

nipy_diagnose — Calculate and write results for diagnostic screen

like. that's the whole job. calculate stuff, write stuff, look cute doing it. periodt. 💅

🎀 SYNOPSIS 🎀

nipy_diagnose [-h] [--out-path OUT_PATH]
[--out-fname-label OUT_FNAME_LABEL] [--ncomponents NCOMPONENTS]
[--time-axis TIME_AXIS] [--slice-axis SLICE_AXIS] filename

🦋 DESCRIPTION 🦋

so nipy_diagnose(1) will generate a series of diagnostic images for a 4D fMRI image volume. no cap, it just cranks out a whole little photoshoot for your data. 💖

the following images will be generated, and <ext> is the input filename extension (e.g. '.nii'):

  • components_<label>.png : plots of PCA basis vectors
  • max_<label><ext> : max image
  • mean_<label><ext> : mean image
  • min_<label><ext> : min image
  • pca_<label><ext> : 4D image of PCA component images
  • pcnt_var_<label>.png : percent variance scree plot for PCA components
  • std_<label><ext> : standard deviation image
  • tsdiff_<label>.png : time series diagnostic plot

iconic lineup honestly. 🫶

the filenames for the outputs are of the form <out-path>/<some_prefix><label><file-ext> where:

  • <out-path> is the path specified by the --out-path option, or the path of the input filename
  • <some_prefix> are the standard prefixes above
  • <label> is given by --out-label, or by the filename of the input image (with path and extension removed)
  • <file-ext> is '.png' for graphics, or the extension of the input filename for volume images

for example, specifying only the input filename /some/path/fname.img will generate filenames of the form /some/path/components_fname.png, /some/path/max_fname.img etc.

see how it just knows?? main character energy fr fr. 👑

✨ OPTIONS ✨

🌈 POSITIONAL ARGUMENTS

  • filename — 4D image filename

💜 OPTIONAL ARGUMENTS

  • -h, --help — Show a help message and exit
  • --out-path OUT_PATH — Path for output image files
  • --out-fname-label OUT_FNAME_LABEL — Mid part of output image filenames
  • --ncomponents NCOMPONENTS — Number of PCA components to write
  • --time-axis TIME_AXIS — Image axis for time
  • --slice-axis TSLICE_AXIS — Image axis for slice
ngl bestie, peep that last one: the option is --slice-axis but the value it takes is written as TSLICE_AXIS in the original. that's not a typo on my end, that's literally what it says, so I'm leaving it exactly as-is. 💀 keep it in mind if you're scripting this.

🌟 SEE ALSO 🌟

nipy_3dto4d(1), nipy_4d_realign(1), nipy_4dto3d(1), nipy_tsdiffana(1)

go read those too, they're the rest of the friend group. 🎀

and that's the whole page, bestie!! this one's from February 2023, page NIPY_DIAGNOSE(1) — tysm for reading, go diagnose something gorgeous, mwah 💖✨🦋

📦 where this page comes from