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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