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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