Dear Saad,
Thanks a lot for your answer. I took my ROIs from different atlases (Harvard-Oxford, STN atlas and BNST mask from https://afni.nimh.nih.gov/BNSTM_Atlas), I thresholded them at different values using fslmaths, and I then registered them to T1 space using ANTs.
I copy here the header information of the thresholded ROIs and the warped ROIs:
ROI in MNI SPACE:
size of header 348
data_type FLOAT32
dim0 3
dim1 364
dim2 436
dim3 364
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 -1.000000
pixdim1 0.500000
pixdim2 0.500000
pixdim3 0.500000
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 MNI_152
qform_code 4
qto_xyz:1 -0.500000 0.000000 -0.000000 90.000000
qto_xyz:2 0.000000 0.500000 -0.000000 -126.000000
qto_xyz:3 0.000000 0.000000 0.500000 -72.000000
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 MNI_152
sform_code 4
sto_xyz:1 -0.500000 0.000000 0.000000 90.000000
sto_xyz:2 0.000000 0.500000 0.000000 -126.000000
sto_xyz:3 0.000000 0.000000 0.500000 -72.000000
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 6.0.0
aux_file
ROI in T1 SPACE:
size of header 348
data_type FLOAT64
dim0 4
dim1 153
dim2 191
dim3 178
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units Unknown
datatype 64
nbyper 8
bitpix 64
pixdim0 1.000000
pixdim1 1.000000
pixdim2 0.976600
pixdim3 0.976600
pixdim4 1.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
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 1.000000 0.000000 0.000000 -76.000000
qto_xyz:2 0.000000 0.976600 0.000000 -92.776993
qto_xyz:3 0.000000 0.000000 0.976600 -86.429100
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
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
Do you think that there is a problem there then? Is what you see here consistent with what you thought about a wrong qform? (or sform?)
Best,
Sam
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