Hi Taylor,
Thanks for your reply.
What I did was:
Using FSL6.0.1 I run:
flirt -ref maskedb0.nii -in t2_M-CRIB_template.nii.gz -omat aff_fsl601.mat -out result_fsl601.nii.gz
the ref is a B0 image (neonatal) and the in is the t2_M-CRIB_template.nii.gz (T2w high resolution neonatal template), the aff_fsl601.mat is:
0.8777373352 -0.04975066455 -0.1264223669 47.68293729
0.03503861778 0.9497552234 -0.2852872303 43.8491624
0.1218032969 0.3023395572 0.9842849569 -42.41240292
0 0 0 1
Then I moved to the previous installation I have from FSL, the 5.0.11 and I run the same command, and the resulting matrix is:
0.8776957993 -0.0502156383 -0.1253502436 47.64803651
0.03902852451 0.9506376698 -0.2860483021 43.41656114
0.1232217425 0.3039468232 0.9843518324 -42.70741646
0 0 0 1
As you can see, the two matrices are almost identical, in fact I can not visually differentiate the results from one to the other, but the intensity value of the voxels change a little bit. Then when I use this matrices to start a non rigid registration to propagate the labels, the final labels are almost equal, but if I run fslcc with the two labels images the cc is 0.9.
The fslhd for these two images is:
filename maskedb0.nii
size of header 348
data_type FLOAT32
dim0 3
dim1 128
dim2 128
dim3 50
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 -1.000000
pixdim1 2.000000
pixdim2 2.000000
pixdim3 2.000000
pixdim4 1.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
toffset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Aligned Anat
qform_code 2
qto_xyz:1 -2.000000 0.000000 -0.000000 0.000000
qto_xyz:2 0.000000 2.000000 -0.000000 -0.000000
qto_xyz:3 0.000000 0.000000 2.000000 -0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Aligned Anat
sform_code 2
sto_xyz:1 -2.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 2.000000 0.000000 -0.000000
sto_xyz:3 0.000000 0.000000 2.000000 -0.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL4.1
aux_file
(This was processed long time ago)
filename t2_M-CRIB_template.nii.gz
size of header 348
data_type FLOAT32
dim0 3
dim1 304
dim2 304
dim3 157
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units Unknown
datatype 16
nbyper 4
bitpix 32
pixdim0 -1.000000
pixdim1 0.629961
pixdim2 0.629961
pixdim3 0.629961
pixdim4 0.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
toffset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Aligned Anat
qform_code 2
qto_xyz:1 -0.628763 -0.034053 -0.018635 102.928627
qto_xyz:2 -0.034025 0.629039 -0.001434 -109.950783
qto_xyz:3 -0.018686 0.000425 0.629683 -38.462326
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Aligned Anat
sform_code 1
sto_xyz:1 -0.628763 -0.034053 -0.018635 102.928627
sto_xyz:2 -0.034025 0.629039 -0.001434 -109.950783
sto_xyz:3 -0.018686 0.000425 0.629683 -38.462326
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
I repeated the experiment, using other atlas of less resolution and the results in that case are identical. Do you know what could be the explanation?
Best regards,
Manuel
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