[Camino-users] bg mask track error
Curci Marina Carmela
marina.curci at epfl.ch
Wed Jul 11 06:14:01 PDT 2012
Hello to everyone!!
I'm running DTI and deterministic tractography on 2 different datasets with 2 different resolutions.
Because of the seedfile has different dimensions from input file I use the option -header and I use also the option -bgmask using as background mask the white matter mask.
This method works well with one dataset, but not with the other one, because I receive the following error:
'Brain mask must be in the same voxel space as the input data'
I suppose there is a sort of conflict between the bgmask and the dataset, but I don't understand the problem.
I estimate the diffusion tensor using the bgmask but I don't have any kind of problem.
Could you help me please??
Maybe the headers could be useful for you:
DATASET WITH ERROR
DATASET (argument for option -header)
sizeof_hdr 348
data_type INT16
dim0 4
dim1 128
dim2 128
dim3 36
dim4 65
dim5 0
dim6 0
dim7 0
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 3.0000000000
pixdim4 8.1000003815
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
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 -1.999997 -0.003654 0.000000 130.620819
qto_xyz:2 0.003654 -1.999997 0.000000 138.607727
qto_xyz:3 0.000000 0.000000 3.000000 -24.710392
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip SIEMENS TrioTim 3T
BGMASK
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 128
dim2 128
dim3 36
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 3.0000000000
pixdim4 1.0000000000
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 Scanner Anat
qform_code 1
qto_xyz:1 -1.999997 -0.003654 0.000000 130.620819
qto_xyz:2 0.003654 -1.999997 0.000000 138.607758
qto_xyz:3 0.000000 0.000000 3.000000 -24.710392
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.999997 -0.003654 0.000000 130.620819
sto_xyz:2 0.003654 -1.999997 0.000000 138.607758
sto_xyz:3 0.000000 0.000000 3.000000 -24.710392
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Anterior-to-Posterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL4.1
DATASET WITHOUT ERROR
DATASET(argument for option -header)
sizeof_hdr 348
data_type INT16
dim0 4
dim1 96
dim2 96
dim3 34
dim4 21
dim5 0
dim6 0
dim7 0
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 2.2083332539
pixdim2 2.2083332539
pixdim3 3.0000000000
pixdim4 6.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
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 -2.208333 0.000000 0.000000 107.204773
qto_xyz:2 0.000000 -2.208333 0.000000 118.048157
qto_xyz:3 0.000000 0.000000 3.000000 -36.849396
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip SIEMENS TrioTim 3T
BGMASK
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 96
dim2 96
dim3 34
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 2.2083332539
pixdim2 2.2083332539
pixdim3 3.0000000000
pixdim4 1.0000000000
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 Scanner Anat
qform_code 1
qto_xyz:1 -2.208333 0.000000 0.000000 107.204773
qto_xyz:2 0.000000 -2.208333 0.000000 118.048149
qto_xyz:3 0.000000 0.000000 3.000000 -36.849396
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -2.208333 0.000000 0.000000 107.204773
sto_xyz:2 0.000000 -2.208333 0.000000 118.048149
sto_xyz:3 0.000000 0.000000 3.000000 -36.849396
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Anterior-to-Posterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL4.1
Thank you for your availability,
Marina
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