Visualize Clusters on Volume

In [1]:

    

%matplotlib inline


    

In [2]:

    

# Voxel cluster extend
cluster_extend = 20

# Threshold for statistical map
threshold = 2.3

# Template to use for background
template = '../scripts/templates/MNI152_T1_1mm_brain.nii.gz'

# Creat CSV file with cluster information
create_CSV = True

# Show cross on cut position
show_cross = True

# Show image annotation (hemisphere laterality and coordination)
annotate_figure = True

# Show colorbar
show_colorbar = True

# Colorbar orientation
colorbar_orientation = 'horizontal'

# Show cluster information in title
show_title = False

# Image resolution
dpi = 300

# Image type
imageType = 'png'

# Add prefix to image name
prefix = 'cluster'


    

In [13]:

    

%run ../scripts/show_cluster_in_volume.py --help


    

    




usage: show_cluster_in_volume.py [-h] [-ce, --cluster_extent cluster_extent]
                                 [-t, --cluster_thr threshold] [--csv]
                                 [--cluster_title] [-c cmap] [-cb]
                                 [--black_bg] [--dpi dpi] [--format format]
                                 stats_file

Show the locations of clusters in a statistical map in MNI space.

positional arguments:
  stats_file            3D nifti file in MNI space containing the statistical values
                         you want to visualise.
                        Note that this file can be pre-thresholded or not.
                        If your file is already thresholded then you will need to
                         pass an argument to the -t option otherwise it will default to 2.3.
                         A suggested value is 0.01.

optional arguments:
  -h, --help            show this help message and exit
  -ce, --cluster_extent cluster_extent
                        Minimum cluster extent for a region to be included in the visualisation
                         (integer)
                         Default: 20
  -t, --cluster_thr threshold
                        Minimum statistical value for a region to be included in the visualisation
                         (float)
                         Default: 2.3
  --csv                 Create a csv file with cluster information.
                         Default: False
  --cluster_title       Show cluster information in the title of the plot.
                         Default: False
  -c cmap, --cmap cmap  Any matplotlib colormap listed at
                          http://matplotlib.org/examples/color/colormaps_reference.html
                         Default: RdBu_r
  -cb, --cbar           Display a colorbar on the right of the plots
                         Default: False
  --black_bg            Set the background to black.
                         Default: White
  --dpi dpi             DPI of output png file
                         Default: 300
  --format format       Format of the output image file.
                         Eg: png, pdf, tif, jpeg, svg. 
                         Default: png

Author: Kirstie Whitaker <kw401@cam.ac.uk>

In [ ]:

    

%run ../scripts/show_volume.py \
    $cluster_extend \
    $threshold \
    $template \
    $create_CSV \
    $show_cross \
    $annotate_figure \
    $show_colorbar \
    $colorbar_orientation \
    $show_title \
    $dpi \
    $imageType \
    $prefix


    

In [ ]:

    

from IPython.display import Image, display
outputs = sorted(gg('figures/*/*.%s' % imageType))
for o in outputs:
    a = Image(filename=o)
    display(a)