[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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