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
pixdim00.00
pixdim13.75
pixdim23.75
pixdim34.00
pixdim41.00
pixdim51.00
pixdim61.00
pixdim71.00
vox_offset 352
cal_max0.
cal_min0.
scl_slope 0.00
scl_inter 0.00
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start0
slice_end 0
slice_duration 0.00
time_offset0.00
intent Unknown
intent_code0
intent_name
intent_p1 0.00
intent_p2 0.00
intent_p3 0.00
qform_name Unknown
qform_code 0
qto_xyz:1 3.75 0.00 0.00 0.00
qto_xyz:2 0.00 3.75 0.00 0.00
qto_xyz:3 0.00 0.00 4.00 0.00
qto_xyz:4 0.00 0.00 0.00 1.00
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.00 0.00 0.00 0.00
sto_xyz:2 0.00 0.00 0.00 0.00
sto_xyz:3 0.00 0.00 0.00 0.00
sto_xyz:4 0.00 0.00 0.00 0.00
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descripFSL3.3
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
pixdim00.00
pixdim10.937500
pixdim20.937500
pixdim31.200477
pixdim41.00
pixdim51.00
pixdim61.00
pixdim71.00
vox_offset 352
cal_max7638.
cal_min0.
scl_slope 1.00
scl_inter 0.00
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start0
slice_end 0
slice_duration 0.00
time_offset0.00
intent Unknown
intent_code0
intent_name
intent_p1 0.00
intent_p2 0.00
intent_p3 0.00
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -0.937500 0.00 -0.00 131.00
qto_xyz:2 0.00 0.937500 -0.00 -119.197502
qto_xyz:3 0.00 0.00 1.20 -77.393600
qto_xyz:4 0.00 0.00 0.00 1.00
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 0.00 0.00 131.00
sto_xyz:2 0.00 0.937500 0.00 -119.197502
sto_xyz:3 0.00 0.00 1.20 -77.393600
sto_xyz:4 0.00 0.00 0.00 1.00
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descripFSL3.3
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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