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Subject:

shift after resampling

From:

Joerg Magerkurth <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 25 Jan 2007 12:42:56 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (49 lines)

Hi,

it's a simple Problem: I want to rotate a high-res anatomy VMR with the
inverse matrix which I got from the corregistration, into the direction of
the corregistration input VMR, with changing the voxelsize and FOV.

The high-res anatomy VMR has the following parameters:
Voxelsize: -1 1,05625 1,05625
DIM: 160 256 256

The input VMR
Voxelsize: -0,9375 0,9375 6,5
DIM: 204 256 19

The size of the output VMR:
Voxelsize: -1 1 1 
DIM: 240 240 256


My procedure:
-corregistrate the anatomy with the input VMR (works!)
-invert the corregistrationmatrix (works!)

-calculate the shift:
 X_shift=(240-204*0,9375)/2=24,375
 y_shift=(240-256*0,9375)/2=0
 z_shift=(256-19*6,5)/2=66,25

-make an identity matrix with the shifts (matrix.mtx)
 1 0 0 24,375
 0 1 0 0
 0 0 1 66,25
 0 0 0 1

-use: convert_xfm -omat temp.mtx concat inverse_coregist.mtx matrix.mtx

-make an fake header with the new resolution: avwcreatehd 240 240 256 1 1 1
 1 1 0 0 0 2 temp.hdr

- use flirt to reorient:
 flirt -in anatomy -applyxfm -init temp.mtx -out output -paddingsize 0.0 
 -interp trilinear -ref temp.hdr

the last step runs wihtout error. But the output has a shift in the positive
y-direction. Why? The FOV in this direction doesn't change, only the voxelsize!

Best regards

Joerg

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