Hi, I am using SCToolbox to register spinal cords of rodents. We have our template for this study and it seems to run fine until we try applying anat2template.nii.gz to other files.
The error I get is “anat2template.nii.gz is invalid: should be encoded in a 5D file with vector intent code (see https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h”
Here is the return of fslhd on anat2template.nii.gz file.
filename anat2template.nii.gz
size of header 348
data_type FLOAT64
dim0 3
dim1 111
dim2 88
dim3 580
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units Unknown
datatype 64
nbyper 8
bitpix 64
pixdim0 -1.000000
pixdim1 0.050000
pixdim2 0.050000
pixdim3 0.150000
pixdim4 1.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
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
toffset 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 -0.050000 0.000000 -0.000000 5.500000
qto_xyz:2 0.000000 0.050000 -0.000000 -0.000000
qto_xyz:3 0.000000 0.000000 0.150000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
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 1.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip
aux_file
I found a previous thread but didn’t find an answer there. Here is what I ran
#register to the template
sct_register_to_template \
-i $infile \
-s $label \
-param step=0,type=label,dof=Tx_Ty_Tz_Sz:step=1,type=im,algo=rigid,metric=MeanSquares,iter=3,smooth=0,gradStep=0.5,slicewise=0,smoothWarpXY=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=3,gradStep=0.5,slicewise=0 \
-t $ourtemplate \
-v 2 \
-lspinal $label \
-ofolder reg/
sct_register_multimodal \
-i $img1 \
-d $img2 \
-o reg.nii.gz \
-param step=1,type=im,algo=translation,slicewise=0,metric=MI,iter=10,gradStep=0.5:step=2,type=im,algo=bsplinesyn,slicewise=0,metric=MI,iter=20,gradStep=0.5,deformation=1x1x0 \
-v 2 \
-ofolder t2startTOt2 \
-owarp warp_t2startTOt2.nii.gz \
-r 0
sct_apply_transfo \
-i $file \
-d $ourtemplate \
-w warp1.nii.gz anat2template.nii.gz \
-o out.nii.gz
I am getting that error when running “sct_apply_transfo.”
Please help! Thanks!