Hello
I meet a problem to use FLIRT to transform a mask
(GroupAverage3D_AxiaMask.nii.gz)
from the group average space
(GroupAverage3D.nii.gz)
to the individual space
(struct_brain.nii.gz).
Their spatial resolutions are listed here:
group_average_space (resolution=2x2x2, dims=91x109x91x1),
individual_space (resolution=1x1x1, dims=160x256x256x1),
mask (resolution=2x2x2, dims=91x109x91x1).
The details of avwinfo are added at the end of this email.
Using FLIRT, the transform matrix from individual_space to
group_average_space was calculated. The inverse matrix was obtained by
using 'convert_xfm'.
By following Item_58 of FSL_faq at
<http://www.fmrib.ox.ac.uk/fslfaq/#flirt_notwork>,
I converted the mask from group_average_space to individual_space, and
named the obtained mask as 'SagMask8359'. The reference was
'individual_space'.
Uisng FSLview to open the obtained mask, 'SagMask8359', I found that the
voxel size of the obtained mask is not (1mm x 1mm x 1mm), the resolution
of the reference space (individual_space), though the result of avwinfo
showed the dimension of the obtained mask is same as that of the
individual space.
I also tried using ApplyXFM to convert the obtained mask 'SagMask8359'
through changing the option 'Based on: Voxlel Dimensions, 160x256x256 and
1x1x1'. Checking it with FSLview, the voxel size are still not exactly
1x1x1.
Any comments and suggestions please,
rhuang
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>>> avwinfo GroupAverage3D.nii.gz
dim1 91
dim2 109
dim3 91
dim4 1
datatype 16
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 105.0000
cal_min 0.0000
file_type NIFTI-1+
>>> avwinfo struct_brain.nii.gz
dim1 160
dim2 256
dim3 256
dim4 1
datatype 4
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
cal_max 550.0000
cal_min 16.0000
file_type NIFTI-1+
>>> avwinfo GroupAverage3D_AxiaMask.nii.gz
dim1 91
dim2 109
dim3 91
dim4 1
datatype 4
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 2.0000000000
pixdim4 1.0000000000
cal_max 4.0000
cal_min 0.0000
file_type NIFTI-1+
>>> avwinfo SagMask8359.nii.gz (not binaried)
dim1 160
dim2 256
dim3 256
dim4 1
datatype 64
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.0000000000
pixdim4 1.0000000000
cal_max 4.0000
cal_min 0.0000
file_type NIFTI-1+
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