NORM - Normalization of image/volume using average and deviation ||

(9/28/12)

PURPOSE

Normalize images/volumes using average and standard deviation, either overall average or average of background outside a mask. For each pixel/voxel it subtracts average and divides by standard deviation. Can operate on a file series. Can use a selection doc file for image numbers.   Example.

SEE ALSO

AR SCA [Arithmetic scaling of image]
AR [Arithmetic operation]
NEG [Negate - invert contrast of image]

USAGE

.OPERATION: NORM [no][avg],[std]
[When used with a single image the optional output registers receive:
First register -- Number of pixels used in average
Second register -- Average.
Third register -- Standard deviation.]

.INPUT FILE NAME OR TEMPLATE: data_unnorm_001@*
[Enter the name of the input image/s.]

If the input file name contains astericks for set of images, SPIDER asks:


.FILE NUMBERS OR SELECTION DOC. FILE NAME: 1-[num]

.MASK (* IF NO MASK) FILE: maskimg
[Enter the name of mask for background area. If no mask is used then the average and standard deviation are calculated over the whole image. Areas with mask value > 0.5 are NOT used in calculating average and standard deviation.]

.OUTPUT FILE NAME OR TEMPLATE: data_norm_001@*
[Enter the name of the output image/s.]

For a 2D image, SPIDER asks:


.APPLY FLAT-FIELD RAMP (Y,N): Y
[If 'Y' then a flat-field ramp is calculated over any non-masked area (mask value < 0.5) and applied to the image prior to normalization.]

SUBROUTINES

UTIL_1010, RAMP_P, NORM3

CALLER

TSWITCH

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