mask_map#

qx_utilities.general.palm.mask_map(image=None, masks=None, output=None, minv=None, maxv=None, join='OR')#

mask_map image=<image file> masks=<list of masks to use> [output=<output image name>] [minv=<list of thresholds>] [maxv=<list of thresholds>] [join=<OR or AND>]

Mask CIFTI images using provided masks and thresholds.

Parameters

--image (str):

The image file to be masked.

--masks (str):

A comma separated list of masks to be used.

--output (str, default None):

An optional image name for the resulting masked image, if none is provided the original image name will be used with tail "_masked" appended.

--minv (str, default None):

The minimum threshold value.

--maxv (str, default None):

The maximum threshold value.

--join (str, default 'OR'):

Whether multiple masks should be joined using logical OR or logical AND operator.

Notes

If more than one mask is provided, the final mask used can be either the intersection of all the individual masks (logical AND) or a union of all the individual masks (logical OR).

Thresholds

At least minv or maxv needs to be specified.

  • If only minv is given, images will be masked with: mask >= minv.

  • If only maxv is given, images will be masked with: mask <= maxv.

  • If both are given, images will be masked with: minv <= mask <= maxv.

If there is just one minv or maxv value, all the masks will be thresholded using the same value. If more values are provided as comma separated list, they should match the number of masks.

mask_map is a wb_command wrapper that enables easy masking of CIFTI images (e.g. ztstat image from PALM), using the provided list of mask files (e.g. p-values imaages from PALM) and thresholds. More than one mask can be used in which case they can be combined using a logical OR or AND operator.

Examples

qunex mask_map image=sustained_anova_reg_zfstat_C0.dscalar.nii \
    masks="FU3s_sustained_anova_tfce_zfstat_fwep_C0.dscalar.nii" \
    maxv=0.017