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FSL  January 2012

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Subject:

Re: invwarp error

From:

Ian Ballard <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 16 Jan 2012 22:54:56 +0000

Content-Type:

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text/plain (90 lines)

Hello,
I am having almost exactly the same problem as below.  I am running featquery after normalizing with FNIRT and it is working on all but 1 subject (I get the same error message listed in the post below).  Normalization and BET results appear fine for this subject. I adding the --force and -v to invwarp in the invfeatreg script.  The script runs, but gets stuck and never finishes. Here is the output:
Found nonlinear warp field...starting warp field inversion...
warp=highres2standard_warp out=highres2standard_warp_inv ref=highres stdvol= args= -v
Extracting ROI
 
WARNING!! Reference image has large non-zero ROI. Check that BET has run successfully on this.
 
Enlarging initial ROI: 0 211 0 213 0 153 0 1 
Enlarged ROI: 0 213 0 215 0 155
Making tmp directory
Generating field
Extracting ROI and offsetting field
Running real INVWARP

Here is some more info that may be useful:
fslstats highres.nii.gz -w
0 211 0 213 0 153 0 1 

fslhd highres.nii.gz
filename       highres.nii.gz

sizeof_hdr     348
data_type      FLOAT32
dim0           3
dim1           256
dim2           256
dim3           166
dim4           1
dim5           1
dim6           1
dim7           1
vox_units      mm
time_units     s
datatype       16
nbyper         4
bitpix         32
pixdim0        0.0000000000
pixdim1        0.9375000000
pixdim2        0.9375000000
pixdim3        1.0000000000
pixdim4        1.0000000000
pixdim5        0.0000000000
pixdim6        0.0000000000
pixdim7        0.0000000000
vox_offset     352
cal_max        3562.0000
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  119.062248
qto_xyz:2      0.000000  0.937500  -0.000000  -88.976250
qto_xyz:3      0.000000  0.000000  1.000000  -70.207603
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     Aligned Anat
sform_code     2
sto_xyz:1      -0.937351  0.016408  0.003398  114.482376
sto_xyz:2      0.016413  0.937355  0.001619  -88.731491
sto_xyz:3      0.003158  -0.001573  0.999993  -73.592857
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        FSL4.0
aux_file     

Thank you for your help,
Ian

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