Hi Andrew,
Attached, the output of my conversion.
I too run mnc2nii without specfying any options.
Naj
On Sat, 18 Aug 2007, Andrew Janke wrote:
> > > What utility are you using to convert minc to nii? (that makes
> > > busted nifti files).
> >
> > mnc2nii
>
> OK, now you have my attention.
>
> Najmeh,
>
> What do you get when you run:
>
> mnc2nii in.mnc out.hdr
> mnc2nii in.mnc out.nii
>
> Where in.mnc is your input MINC file before conversion to
> NIFTI/ANALYZE. I get this:
>
> gordon:~$ ls -l out.*
> -rw-r--r-- 1 rotor rotor 348 2007-08-18 02:09 out.hdr
> -rw-r--r-- 1 rotor rotor 28436548 2007-08-18 02:09 out.img
> -rw-r--r-- 1 rotor rotor 28436896 2007-08-18 02:09 out.nii
>
>
> --
> Andrew Janke ([log in to unmask] || http://a.janke.googlepages.com/)
> Canberra->Australia +61 (402) 700 883
>
[najma@rosaline ~/cort/DTI_workspace_yongHe/DTI_tracks_AUCGAM]% mnc2nii left_120 .mnc left_120_test.nii
<nifti_image
nifti_type = 'NIFTI-1+'
header_filename = 'left_120_test.nii'
image_filename = 'left_120_test.nii'
image_offset = '0'
ndim = '3'
nx = '91'
ny = '109'
nz = '91'
dx = '2'
dy = '2'
dz = '2'
datatype = '16'
datatype_name = 'FLOAT32'
nvox = '902629'
nbyper = '4'
byteorder = 'LSB_FIRST'
scl_slope = '0.00392157'
scl_inter = '0'
xyz_units = '2'
xyz_units_name = 'mm'
time_units = '8'
time_units_name = 's'
descrip = 'mnc2nii left_120.mnc left_120_test.nii'
sform_code = '1'
sform_code_name = 'Scanner Anat'
sto_xyz_matrix = '2 0 0 -90 -0 2 0 -126 -0 0 2 -72 0 0 0 1'
sto_ijk matrix = '0.5 0 0 45 0 0.5 -0 63 0 -0 0.5 36 0 0 0 1'
sform_i_orientation = 'Left-to-Right'
sform_j_orientation = 'Posterior-to-Anterior'
sform_k_orientation = 'Inferior-to-Superior'
/>
MINC type 5 signed 1
0: 91 0 1
1: 109 1 1
2: 91 2 -1
bytes per voxel 4
# of voxels 902629
0 0 0 => -90.000000 -126.000000 -72.000000
10 0 0 => -70.000000 -126.000000 -72.000000
0 10 0 => -90.000000 -106.000000 -72.000000
0 0 10 => -90.000000 -126.000000 -52.000000
10 10 10 => -70.000000 -106.000000 -52.000000
.mnc left_120_test.hdr
<nifti_image
nifti_type = 'NIFTI-1'
header_filename = 'left_120_test.hdr'
image_filename = 'left_120_test.img'
image_offset = '0'
ndim = '3'
nx = '91'
ny = '109'
nz = '91'
dx = '2'
dy = '2'
dz = '2'
datatype = '16'
datatype_name = 'FLOAT32'
nvox = '902629'
nbyper = '4'
byteorder = 'LSB_FIRST'
scl_slope = '0.00392157'
scl_inter = '0'
xyz_units = '2'
xyz_units_name = 'mm'
time_units = '8'
time_units_name = 's'
descrip = 'mnc2nii left_120.mnc left_120_test.hdr'
sform_code = '1'
sform_code_name = 'Scanner Anat'
sto_xyz_matrix = '2 0 0 -90 -0 2 0 -126 -0 0 2 -72 0 0 0 1'
sto_ijk matrix = '0.5 0 0 45 0 0.5 -0 63 0 -0 0.5 36 0 0 0 1'
sform_i_orientation = 'Left-to-Right'
sform_j_orientation = 'Posterior-to-Anterior'
sform_k_orientation = 'Inferior-to-Superior'
/>
MINC type 5 signed 1
0: 91 0 1
1: 109 1 1
2: 91 2 -1
bytes per voxel 4
# of voxels 902629
0 0 0 => -90.000000 -126.000000 -72.000000
10 0 0 => -70.000000 -126.000000 -72.000000
0 10 0 => -90.000000 -106.000000 -72.000000
0 0 10 => -90.000000 -126.000000 -52.000000
10 10 10 => -70.000000 -106.000000 -52.000000
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