First release to test pypi
Project description
nifti-snapshot
Tools used to summarize nifti files into figures.
git clone https://github.com/pnlbwh/nifti-snapshot
Contents
- TODO
- Dependencies
- TBSS figures
TODO
- test script
- add different background image options
- 4d map summary (diffusion)
- ROI & multi ROI visualization
- project wise examples
Dependencies
FSLDIR in PATH
ENIGMA_dir in PATH
# download from http://enigma.ini.usc.edu/wp-content/uploads/2013/02/enigmaDTI.zip
python 3.7
scipy==1.3.3
nibabel==2.4.0
numpy==1.16.2
pathlib2==2.3.3
matplotlib==3.0.3
Single image examples
Link to a single image examples
TBSS figures
From commandline
Snapshot of an tbss_fill
image
fw=tbss_FW_tfce_corrp_tstat2_filled.nii.gz
./nifti_snapshot \
--input ${fw} \
--tbss \
--output_file cli_test_fw.png \
--cmap "Blues_r" \
--title "Significant changes in FW in group A" \
--cbar_title 'Increased FW'
Snapshot of two tbss_fill
images with overlap highlight
fa=tbss_FA_tfce_corrp_tstat1_filled.nii.gz
fat=tbss_FAt_tfce_corrp_tstat1_filled.nii.gz
./nifti_snapshot \
--input ${fa} ${fat} \
--tbss \
--output_file cli_test.png \
--cmap "Blues_r" "autumn" \
--title "Significant changes in FA and FAt in group A" \
--cbar_title 'Reduced' 'Reduced FAt' 'Overlap' \
--overlap \
--overlap_cmap "summer" \
--overlap_alpha 0.8
From python
Snapshot of an tbss_fill
image
from nifti_snapshot import nifti_snapshot
fw = 'tbss_FA_tfce_corrp_tstat1_filled.nii.gz'
fw_color = 'Blues_r'
tbssFigure = nifti_snapshot.TbssFigure(
image_files=[fw],
output_file='docs/fw_example.png',
cmap_list=[fw_color],
cbar_titles=['Increased FW'],
alpha_list=[0.8],
title='Increased Freewater in group A',
cbar_x=0.35, cbar_width=0.3)
tbssFigure.create_figure_one_map()
Snapshot of two tbss_fill
images with overlap highlight
from nifti_snapshot import nifti_snapshot
fa = 'tbss_FA_tfce_corrp_tstat1_filled.nii.gz'
fat = 'tbss_FAt_tfce_corrp_tstat1_filled.nii.gz'
fa_color_1 = 'Blues_r'
fa_color_2 = 'autumn'
fa_color_overlap = 'summer'
tbssFigure = nifti_snapshot.TbssFigure(
image_files=[fa, fat],
output_file='docs/fa_fat_example.png',
cmap_list=[fa_color_1, fa_color_2],
overlap_cmap=fa_color_overlap,
cbar_titles=[
'Reduced FA',
'Reduced FAt',
'Overlap'],
alpha_list=[1, 1, 0.8],
title='Significant changes in FA and FAt in group A')
tbssFigure.create_figure_two_maps_and_overlap()
Project details
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nifti_snapshot-0.1.8.tar.gz
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