Hi all,
I am trying to mask one image with another using fslmaths.
I am getting the error:
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
I suspect that it is due to the header files being slightly different (attached to the end of this mail).
The two files were created in two different programmes (FSL and Freesurfer) and the header information is very slightly different for each file.
Can I safely ignore this warning?
The results that I am seeing are as expected and it is not crucial that the masking be perfect but I just get very wary when I start seeing error messages.
Regards,
Claude
HEADER 1:
filename _03DN_lh_G_and_S_cingul-Ant.nii.gz
sizeof_hdr 348
data_type INT32
dim0 3
dim1 128
dim2 128
dim3 60
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 8
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 1.8750000000
pixdim2 1.8750000000
pixdim3 2.0999999046
pixdim4 0.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
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
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.875000 0.000664 0.000000 119.092148
qto_xyz:2 0.000664 1.875000 0.000453 -119.117523
qto_xyz:3 -0.000000 -0.000405 2.100000 -61.385921
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 Scanner Anat
sform_code 1
sto_xyz:1 -1.875000 0.000664 0.000000 119.092148
sto_xyz:2 0.000664 1.875000 0.000453 -119.117523
sto_xyz:3 0.000000 -0.000405 2.100000 -61.385921
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 FreeSurfer Feb 26 2013
aux_file
HEADER 2:
filename gwi.nii
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 128
dim2 128
dim3 60
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 1.8750000000
pixdim2 1.8750000000
pixdim3 2.0999999046
pixdim4 0.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
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
time_offset 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 -1.875000 0.000000 -0.000000 119.062500
qto_xyz:2 0.000000 1.875000 -0.000000 -119.062500
qto_xyz:3 0.000000 0.000000 2.100000 -61.949997
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 -1.875000 0.000000 0.000000 119.062500
sto_xyz:2 0.000000 1.875000 0.000000 -119.062500
sto_xyz:3 0.000000 0.000000 2.100000 -61.949997
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 FSL5.0
aux_file
