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Hi Manuel, This is fine. These minor differences are to be expected when the underlaying maths library has been changed (which is the case for fsl 6 vs FSL 5.0.11. Cheers, Taylor Hanayik Taylor Hanayik PhD Analysis Research Software Engineer FMRIB, John Radcliffe Hospital University of Oxford [log in to unmask]<mailto:[log in to unmask]> On 17 Jun 2019, at 14:33, Manuel Blesa <[log in to unmask]<mailto:[log in to unmask]>> wrote: 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 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1