SCT v4.3
Hi,
When running ‘sct_register_to_template’, e.g.:
sct_register_to_template -i sc_fmri.nii.gz -s frmi_seg.nii.gz -l fmri_label.nii.gz -c t2s -ref subject
The following “warning” appears, about halfway through the output:
Apply transformation and resample to destination space...
/home/sapgt4/sct_4.3/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_0.txt -r dest_seg_RPI.nii -n NearestNeighbor # in /tmp/sct-20200722164906.795422-register-0mo9smr6
Copy affine matrix from destination space to make sure qform/sform are the same.
WARNING: the resulting image could have wrong apparent results. You should use an affine transformation as last transformation...
I assume this is irrelevant, as the resultant registration looks great.
I’ve not noticed the warning before, but it is quite possible it has always appeared!
So two questions:
- Am I doing something risky that requires a warning?
- Does this ‘warning’ need to appear as part of the ‘sct_register_to_template’ output?
Thanks in advance.
Hi @george_tackley,
I cannot reproduce these warnings with the testing data. First thing to verify: could you please copy/paste the output of:
fslhd sc_fmri
fslhd frmi_seg
fslhd fmri_label
** ORIGINAL POST NOW EDITED TO REFLECT OMISSION OUTLINED BELOW **
Hi @jcohenadad,
Thanks for the reply. Apologies, somehow I trimmed off the ‘-ref subject’ option from the call (which makes all the difference), it should have read:
sct_register_to_template -i sc_fmri.nii.gz -s fmri_seg.nii.gz -l fmri_label.nii.gz -c t2s -ref subject
Header info below.
BW
George
filename sc_fmri.nii.gz
size of header 348
data_type INT16
dim0 3
dim1 40
dim2 40
dim3 20
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 -1.000000
pixdim1 1.230769
pixdim2 1.230769
pixdim3 5.000000
pixdim4 1.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 6096
cal_max 0.000000
cal_min 0.000000
scl_slope 0.014905
scl_inter 488.402466
phase_dim 0
freq_dim 0
slice_dim 3
slice_name Unknown
slice_code 0
slice_start 0
slice_end 19
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 -1.230769 0.000000 -0.000000 24.615368
qto_xyz:2 0.000000 1.119060 2.081404 -30.782221
qto_xyz:3 -0.000000 -0.512346 4.546181 -71.267029
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 1
sto_xyz:1 -1.230769 0.000000 0.000000 24.615368
sto_xyz:2 0.000000 1.119060 2.081404 -30.782221
sto_xyz:3 0.000000 -0.512346 4.546181 -71.267029
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
filename fmri_seg.nii.gz
size of header 348
data_type FLOAT64
dim0 3
dim1 40
dim2 40
dim3 20
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 64
nbyper 8
bitpix 64
pixdim0 -1.000000
pixdim1 1.230769
pixdim2 1.230769
pixdim3 5.000000
pixdim4 1.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 6096
cal_max 0.000000
cal_min 0.000000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 3
slice_name Unknown
slice_code 0
slice_start 0
slice_end 19
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 -1.230769 0.000000 -0.000000 24.615368
qto_xyz:2 0.000000 1.119060 2.081404 -30.782221
qto_xyz:3 -0.000000 -0.512346 4.546181 -71.267029
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 1
sto_xyz:1 -1.230769 0.000000 0.000000 24.615368
sto_xyz:2 0.000000 1.119060 2.081404 -30.782221
sto_xyz:3 0.000000 -0.512346 4.546181 -71.267029
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
filename fmri_label.nii.gz
size of header 348
data_type FLOAT64
dim0 3
dim1 40
dim2 40
dim3 20
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 64
nbyper 8
bitpix 64
pixdim0 -1.000000
pixdim1 1.230769
pixdim2 1.230769
pixdim3 5.000000
pixdim4 1.000000
pixdim5 1.000000
pixdim6 1.000000
pixdim7 1.000000
vox_offset 6096
cal_max 0.000000
cal_min 0.000000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 3
slice_name Unknown
slice_code 0
slice_start 0
slice_end 19
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 -1.230769 0.000000 -0.000000 24.615368
qto_xyz:2 0.000000 1.119060 2.081404 -30.782221
qto_xyz:3 -0.000000 -0.512346 4.546181 -71.267029
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 1
sto_xyz:1 -1.230769 0.000000 0.000000 24.615368
sto_xyz:2 0.000000 1.119060 2.081404 -30.782221
sto_xyz:3 0.000000 -0.512346 4.546181 -71.267029
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
thanks, i can reproduce-- working on it here
You can ignore the warning. It will be silenced in the future version of SCT (see pull request). Thank you for notifying us 