The input file is the output of the AFNI program 3dDeconvolve.
It was converted to nifti format with 3dAFNItoNIFTI command.
(3dAFNItoNIFTI was also used to convert the raw data to nifti,
for with -applyxfm works fine).
Here is the output of avwhd for the input file and for the output
file:
INPUT (statmap):
filename 1225.RLSPDF.bucket.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 5
dim1 64
dim2 64
dim3 36
dim4 1
dim5 322
dim6 1
dim7 1
vox_units mm
time_units Unknown
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 3.2500000000
pixdim2 3.2500000000
pixdim3 3.2999999523
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 22144
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 Scanner Anat
qform_code 1
qto_xyz:1 -3.250000 0.000000 0.000000 102.375000
qto_xyz:2 0.000000 -3.250000 0.000000 132.375000
qto_xyz:3 0.000000 0.000000 3.300000 -27.500000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -3.250000 0.000000 0.000000 102.375000
sto_xyz:2 0.000000 -3.250000 0.000000 132.375000
sto_xyz:3 0.000000 0.000000 3.300000 -27.500000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Anterior-to-Posterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip
aux_file
OUTPUT:
Darwin birdie rhdesai ~/pub/SenLit/sl.1225/AFNIWORK 207: avwhd 1225.RLSPDF.bucket.reg.nii.gz
filename 1225.RLSPDF.bucket.reg.nii.gz
sizeof_hdr 348
data_type FLOAT32
dim0 3
dim1 256
dim2 256
dim3 134
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 16
nbyper 4
bitpix 32
pixdim0 0.0000000000
pixdim1 0.8125000000
pixdim2 0.8125000000
pixdim3 1.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 22144
cal_max 0.0000
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 -0.812500 0.000000 0.000000 103.593803
qto_xyz:2 0.000000 -0.812500 0.000000 133.593994
qto_xyz:3 0.000000 0.000000 1.000000 -40.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Anterior-to-Posterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -0.812500 0.000000 0.000000 103.593803
sto_xyz:2 0.000000 -0.812500 0.000000 133.593994
sto_xyz:3 0.000000 0.000000 1.000000 -40.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Anterior-to-Posterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL3.3
aux_file
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
Sent: Sun 10/22/2006 3:37 PM
To: [log in to unmask]
Subject: Re: [FSL] -applyxfm in flirt
Hi,
This might be due to how the original image (statmap)
was formed. Can you describe how you generated it?
Also, please send us the output of avwhd on the input
and output files.
All the best,
Mark
On 22 Oct 2006, at 05:43, Rutvik Desai wrote:
> I am tring to apply a transformation matrix (calculated
> using flirt) to a statistical parametric map, but the output is
> not correct.
>
> flirt -in statmap.nii -init flirt.mat -applyxfm -ref anat.bet.nii -out
> statmap.reg
>
> The statmap has many datapoints per voxel (t-stats, betas, etc.),
> but the
> resulting statmap.reg has only one datapoint (only one BRIK in
> AFNI jargon) for some reason.
>
> If the same command is run with the raw data as input instead of the
> statmap, the output is correct as expected with all the datapoints.
> Any ideas?
>
> Thanks,
> Rutvik
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