[Camino-users] R: bg mask track error
Curci Marina Carmela
marina.curci at epfl.ch
Wed Jul 11 12:14:30 PDT 2012
Hello....sorry for the spam...It's just to say that I solved my problem...
I have a question: if I run the track command and then procstreamlines using as input for track the pds file, I have noticed that the number of streamlines generated with track is different from the number of streamlines processed by procstreamlines. Could you explain to me the reason, please??
Thank you for your help!!!
Marina
________________________________________
Da: Curci Marina Carmela
Inviato: mercoledì 11 luglio 2012 15.14
A: camino-users at www.nitrc.org
Oggetto: bg mask track error
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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