Easy thresh

CPAC.easy_thresh.copy_geom(infile_a, infile_b)[source]

Method to call fsl fslcpgeom command to copy certain parts of the header information (image dimensions, voxel dimensions, voxel dimensions units string, image orientation/origin or qform/sform info) from one image to another

  • infile_a (nifti file) – input volume from which the geometry is copied from

  • infile_b (nifti file) – input volume from which the geometry is copied to


out_file – Input volume infile_b with modified geometry information in the header.

Return type:

nifti file


Exception – If fslcpgeom fails


Workflow for carrying out cluster-based thresholding and colour activation overlaying


wf_name (string) – Workflow name


easy_thresh – Easy thresh workflow object

Return type:




Workflow Inputs:

inputspec.z_stats : string (nifti file)
    z_score stats output for t or f contrast from flameo

inputspec.merge_mask : string (nifti file)
    mask generated from 4D Merged derivative file

inputspec.z_threshold : float
    Z Statistic threshold value for cluster thresholding. It is used to
    determine what level of activation would be statistically significant.
    Increasing this will result in higher estimates of required effect.

inputspec.p_threshold : float
    Probability threshold for cluster thresholding.

inputspec.paramerters : string (tuple)
    tuple containing which MNI and FSLDIR path information

Workflow Outputs:

outputspec.cluster_threshold : string (nifti files)
   the thresholded Z statistic image for each t contrast

outputspec.cluster_index : string (nifti files)
    image of clusters for each t contrast; the values
    in the clusters are the index numbers as used
    in the cluster list.

outputspec.overlay_threshold : string (nifti files)
    3D color rendered stats overlay image for t contrast
    After reloading this image, use the Statistics Color
    Rendering GUI to reload the color look-up-table

outputspec.overlay_rendered_image : string (nifti files)
   2D color rendered stats overlay picture for each t contrast

outputspec.cluster_localmax_txt : string (text files)
    local maxima text file, defines the coordinates of maximum value
    in the cluster

Order of commands:

  • Estimate smoothness of the image:

    smoothest --mask= merge_mask.nii.gz --zstat=.../flameo/stats/zstat1.nii.gz
    --mask  :  brain mask volume
    --zstat :  filename of zstat/zfstat image
  • Create mask. For details see fslmaths:

    fslmaths ../flameo/stats/zstat1.nii.gz
             -mas merge_mask.nii.gz
    -mas   : use (following image>0) to mask current image
  • Copy Geometry image dimensions, voxel dimensions, voxel dimensions units string, image orientation/origin or qform/sform info) from one image to another:

    fslcpgeom MNI152_T1_2mm_brain.nii.gz zstat1_mask.nii.gz
  • Cluster based thresholding. For details see FEAT:

    cluster --dlh = 0.0023683100
            --in = zstat1_mask.nii.gz
            --oindex = zstat1_cluster_index.nii.gz
            --olmax = zstat1_cluster_localmax.txt
            --othresh = zstat1_cluster_threshold.nii.gz
            --pthresh = 0.0500000000
            --thresh = 2.3000000000
            --volume = 197071
    --in    :    filename of input volume
    --dlh   :    smoothness estimate = sqrt(det(Lambda))
    --oindex  :  filename for output of cluster index
    --othresh :  filename for output of thresholded image
    --olmax   :  filename for output of local maxima text file
    --volume  :  number of voxels in the mask
    --pthresh :  p-threshold for clusters
    --thresh  :  threshold for input volume

Z statistic image is thresholded to show which voxels or clusters of voxels are activated at a particular significance level. A Z statistic threshold is used to define contiguous clusters. Then each cluster’s estimated significance level (from GRF-theory) is compared with the cluster probability threshold. Significant clusters are then used to mask the original Z statistic image.

  • Get the maximum intensity value of the output thresholded image. This used is while rendering the Z statistic image:

    fslstats zstat1_cluster_threshold.nii.gz -R
    -R  : output <min intensity> <max intensity>
  • Rendering. For details see FEAT:

    overlay 1 0 MNI152_T1_2mm_brain.nii.gz
           -a zstat1_cluster_threshold.nii.gz
           2.30 15.67
    slicer zstat1_cluster_threshold_overlay.nii.gz
           -L  -A 750

    The Z statistic range selected for rendering is automatically calculated by default, to run from red (minimum Z statistic after thresholding) to yellow (maximum Z statistic, here maximum intensity).

High Level Workflow Graph:


Detailed Workflow Graph:



>>> from CPAC.easy_thresh import easy_thresh
>>> preproc = easy_thresh("new_workflow")
>>> preproc.inputs.inputspec.z_stats= 'flameo/stats/zstat1.nii.gz'
>>> preproc.inputs.inputspec.merge_mask = 'merge_mask/alff_Z_fn2standard_merged_mask.nii.gz'
>>> preproc.inputs.inputspec.z_threshold = 2.3
>>> preproc.inputs.inputspec.p_threshold = 0.05
>>> preproc.inputs.inputspec.parameters = ('/usr/local/fsl/', 'MNI152')
>>> preporc.run()  
CPAC.easy_thresh.get_standard_background_img(in_file, file_parameters)[source]

Method to get the standard brain image from FSL standard data directory

  • in_file (nifti file) – Merged 4D Zmap volume

  • file_parameters (tuple) – Value FSLDIR and MNI from config file


standard_path – Standard FSL Image file path

Return type:



Exception – If nibabel cannot load the input nifti volume

CPAC.easy_thresh.get_tuple(infile_a, infile_b)[source]

Simple method to return tuple of z_threhsold maximum intensity values of Zstatistic image for input to the overlay.

  • z_theshold (float) – z threshold value

  • intensity_stat (tuple of float values) – minimum and maximum intensity values


img_min_max – tuple of zthreshold and maximum intensity value of z statistic image

Return type:

tuple (float)