Dear FSL experts,
I have 3D nifti files corresponding to one mask image for each hemisphere and for each subject (maybe it's unusual, but these are volumes of activated tissue from Deep Brain Stimulation to each hemisphere)
First, I'm not interested in the side of the brain concerned in my analysis, so I would like to lateralise the Right volumes to the Left using fslswapdim. Then I would like to build 4D files from these using fslmerge.
However, when using fslswapdim (-x y z), I get no error (excepted the warning for flipping Left/Right orientation) but my output files are exactly the same as my input file. Then, using fslmerge, the position of my volumes relative to the MNI template (and thus relative to each other) is lost, which is obviously a great problem. Indeed it seems that the centres of my volumes are aligned while they should not.
I think that it has to do with my nifti files format and maybe with the q and sform_name being 'aligned anat' (I paste the fslhd output below), but I've not been able to solve these issues. Could someone help me ? Thanks
Garance Meyer
Header:
filename 001_AuAr_vat_right.nii
size of header 348
data_type INT16
dim0 3
dim1 100
dim2 100
dim3 100
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 1.000000
pixdim1 0.181818
pixdim2 0.181818
pixdim3 0.252525
pixdim4 0.000000
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
scl_slope 0.000031
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 Aligned Anat
qform_code 2
qto_xyz:1 0.181818 0.000000 0.000000 3.000000
qto_xyz:2 0.000000 0.181818 0.000000 -23.000000
qto_xyz:3 0.000000 0.000000 0.252525 -18.000000
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 Aligned Anat
sform_code 2
sto_xyz:1 0.181818 0.000000 0.000000 3.000000
sto_xyz:2 0.000000 0.181818 0.000000 -23.000000
sto_xyz:3 0.000000 0.000000 0.252525 -18.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip lead dbs - vat
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|