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FSL  June 2019

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Subject:

Re: FSL randomise results changed after re-installing FSL

From:

Manuel Blesa <[log in to unmask]>

Reply-To:

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

Date:

Mon, 17 Jun 2019 14:33:09 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (175 lines)

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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