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_fileyour 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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