Hi All,
I am trying to find the intersection between the mask subtracted.nii.gz and the mask wmxfm.nii.gz using the command
fslmaths subtracted.nii.gz -mas wmxfm.nii.gz subtractedAfter.nii.gz
but it is giving me the warning
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
I have attached the outputs of fslhd on the two files. What exactly is wrong and how do I fix their mismatch in orientations?
Thank you,
Lily
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filename masks/6003_00_10132016/test/subtracted.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 256
dim2 256
dim3 160
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.200000
pixdim4 0.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
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 Scanner Anat
qform_code 1
qto_xyz:1 0.018834 0.040005 1.198826 -98.020523
qto_xyz:2 -0.937337 -0.346991 0.037879 185.168991
qto_xyz:3 -0.347915 0.937015 -0.037156 -84.678329
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Anterior-to-Posterior
qform_yorient Inferior-to-Superior
qform_zorient Left-to-Right
sform_name Scanner Anat
sform_code 1
sto_xyz:1 0.018834 0.040006 1.198826 -98.020523
sto_xyz:2 -0.937337 -0.346991 0.037879 185.168991
sto_xyz:3 -0.347914 0.937015 -0.037156 -84.678329
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Anterior-to-Posterior
sform_yorient Inferior-to-Superior
sform_zorient Left-to-Right
file_type NIFTI-1+
file_code 1
descrip FSL5.0
aux_file
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filename masks/6003_00_10132016/test2/wmxfm.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 256
dim2 256
dim3 160
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.000000
pixdim1 1.000000
pixdim2 1.000000
pixdim3 1.200000
pixdim4 2.510000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
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 0.018834 -0.040006 -1.198826 102.794342
qto_xyz:2 -0.937337 0.346991 -0.037879 102.709137
qto_xyz:3 -0.347914 -0.937015 0.037157 148.352570
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Anterior-to-Posterior
qform_yorient Superior-to-Inferior
qform_zorient Right-to-Left
sform_name Scanner Anat
sform_code 1
sto_xyz:1 0.018834 -0.040006 -1.198826 102.794342
sto_xyz:2 -0.937337 0.346991 -0.037879 102.709137
sto_xyz:3 -0.347914 -0.937015 0.037157 148.352570
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Anterior-to-Posterior
sform_yorient Superior-to-Inferior
sform_zorient Right-to-Left
file_type NIFTI-1+
file_code 1
descrip FreeSurfer Dec 29 2016
aux_file
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