Inputs:
[Mandatory]
data_file : (an existing file name)
ANALYZE img file
header_file : (an existing file name)
corresponding ANALYZE hdr file
[Optional]
affine : (an array)
affine transformation array
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
Outputs:
nifti_file : (an existing file name)
Unknown
Calculates distance between two volumes.
Inputs:
[Mandatory]
volume1 : (an existing file name)
Has to have the same dimensions as volume2.
volume2 : (an existing file name)
Has to have the same dimensions as volume1.
[Optional]
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
method : ('eucl_min' or 'eucl_cog' or 'eucl_mean' or 'eucl_wmean')
""eucl_min": Euclidean distance between two closest points "eucl_cog": mean Euclidian distance between the Center of Gravity of volume1 and CoGs of volume2 "eucl_mean": mean Euclidian minimum distance of all volume2 voxels to volume1 "eucl_wmean": mean Euclidian minimum distance of all volume2 voxels to volume1 weighted by their values
Outputs:
distance : (a float)
Unknown
histogram : (a file name)
Unknown
point1 : (an array with shape (3,))
Unknown
point2 : (an array with shape (3,))
Unknown
Left multiplies the affine matrix with a specified values. Saves the volume as a nifti file.
Inputs:
[Mandatory]
volumes : (an existing file name)
volumes which affine matrices will be modified
[Optional]
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
transformation_matrix : (an array with shape (4, 4))
transformation matrix that will be left multiplied by the affine matrix
Outputs:
transformed_volumes : (a file name)
Unknown
Calculates various overlap measures between two maps.
>>> overlap = Overlap()
>>> overlap.inputs.volume1 = 'cont1.nii'
>>> overlap.inputs.volume1 = 'cont2.nii'
>>> res = overlap.run()
Inputs:
[Mandatory]
volume1 : (an existing file name)
Has to have the same dimensions as volume2.
volume2 : (an existing file name)
Has to have the same dimensions as volume1.
[Optional]
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
out_file : (a file name)
Unknown
Outputs:
dice : (a float)
Unknown
diff_file : (an existing file name)
Unknown
jaccard : (a float)
Unknown
volume_difference : (an integer)
Unknown
Returns ROI masks given an atlas and a list of labels. Supports dilation and left right masking (assuming the atlas is properly aligned).
Inputs:
[Mandatory]
atlas : (an existing file name)
Location of the atlas that will be used.
[Optional]
dilation_size : (an integer)
Defines how much the mask will be dilated (expanded in 3D).
hemi : ('both' or 'left' or 'right')
Restrict the mask to only one hemisphere: left or right
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
labels : (an integer or a list of items which are an integer)
Labels of regions that will be included in the mask. Must be compatible with the atlas used.
output_file : (a file name)
Where to store the output mask.
Outputs:
mask_file : (an existing file name)
output mask file
Inputs:
[Mandatory]
threshold : (a float)
volumes to be thresholdedeverything below this value will be set to zero
volumes : (an existing file name)
volumes to be thresholded
[Optional]
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
Outputs:
thresholded_volumes : (an existing file name)
thresholded volumes
Computes the time-course SNR for a time series
Typically you want to run this on a realigned time-series.
>>> tsnr = TSNR()
>>> tsnr.inputs.in_file = 'functional.nii'
>>> res = tsnr.run()
Inputs:
[Mandatory]
in_file : (an existing file name)
realigned 4D file
[Optional]
ignore_exception : (a boolean)
Print an error message instead of throwing an exception in case the interface fails to run
Outputs:
tsnr_file : (an existing file name)
tsnr image file