What do you mean "to get proper output from reg-feat2anat"? This program
produces a freesurfer registration file, which you then check with reg-feat2anat --manual
...
doug
Vishwadeep Ahluwalia wrote:
Hi,
To elaborate my problem a little more ...
Running FSL command avwhd gave me :
filename spiral.nii.gz
sizeof_hdr 348
data_type INT16
dim0 4
dim1 64
dim2 64
dim3 25
dim4 250
dim5 1
dim6 1
dim7 1
vox_units Unknown
time_units Unknown
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 3.7500000000
pixdim2 3.7500000000
pixdim3 4.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
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 Unknown
qform_code 0
qto_xyz:1 3.750000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 3.750000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 4.000000 0.000000
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 Unknown
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 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FSL3.3
aux_file
And avwhd on the spgr gave me:
filename spgr.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 256
dim2 256
dim3 124
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 0.9375000000
pixdim2 0.9375000000
pixdim3 1.2000000477
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 7638.0000
cal_min 0.0000
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
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 -0.937500 0.000000 -0.000000 131.000000
qto_xyz:2 0.000000 0.937500 -0.000000 -119.197502
qto_xyz:3 0.000000 0.000000 1.200000 -77.393600
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 -0.937500 0.000000 0.000000 131.000000
sto_xyz:2 0.000000 0.937500 0.000000 -119.197502
sto_xyz:3 0.000000 0.000000 1.200000 -77.393600
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 FSL3.3
aux_file
When I analyze the data in FSL I get the expected activation (Left
hemisphere activation for right hand movement)so I know that FSL is reading
or assuming the orientation correctly for the functional(even though sform
and qform are unknown). My question is : after I run the recon-all process
on the spgr, what do I need to do to the functional data to get freesurfer
to read it correctly inorder to get proper output from reg-feat2anat?
Any help is appreciated.
Thanks
Regards,
Vish
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