2D images segmentation

Good morning!
I need to segment spinal cord images from 7T 2D multi-echo FLASH T2*-weighted sequences.
I tried to launch sct_propseg but looks like it needs 3D images.
Can you help?
Thank you,
Valeria

Hi,
what is the output of fslhd YOUR_IMAGE?


sizeof_hdr     348
data_type      FLOAT32
dim0           4
dim1           534
dim2           512
dim3           18
dim4           3
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       16
nbyper         4
bitpix         32
pixdim0        0.000000
pixdim1        0.411985
pixdim2        0.411985
pixdim3        3.600000
pixdim4        0.500000
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      -0.411100  0.000021  -0.235839  110.892990
qto_xyz:2      0.001544  -0.411292  -0.208316  124.242630
qto_xyz:3      -0.026945  -0.023890  3.586221  40.293308
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      -0.411100  -0.000000  -0.235844  110.892990
sto_xyz:2      0.001565  -0.411292  -0.208310  124.242630
sto_xyz:3      -0.026945  -0.023890  3.586221  40.293308
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        FreeSurfer May 13 2013
aux_file

your volume has 4 dimensions: dim0 4. The 4th dimension are the echoes.

you need to compute segmentation on a 3D dataset.

you can reduce the dimensionality by averaging all echoes across time, e.g.:

sct_maths -i 4DIMAGE -mean t -o 3DIMAGE

and then use 3DIMAGE as input for propseg

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