Dear fsl-users,
I used FNIRT to nonlin register my data to the MNI space. Then I tried to bring the MNI152_T1_2mm_brain.nii.gz to T1 space where I encountered the problem with invwarp.
I followed the proposed scheme in the fnirt user guide that is
1) fnirt the Struct.nii to the MNI152_T1_2mm, 2) calculate the invert transform , 3) apply the invert transform to the MNI152_T1_2mm_brain.
In all my data I was given the warning:
WARNING!! Reference image has large non-zero ROI. Check that BET has run successfully on this.
The brain extraction as well as the flirt affine registration looked ok (See attached .txt file with details of fslhd and fslstats -w). So I forced the invert transform to take place ( what it was proposed in the forum under similar cases)
The problem though is that the time needed to calculate the invert transformation became enormous. For one subject it took more than 48 hours in a desktop computer while the average time to calculate the invert tranformation of subjects in the same computer (without a warning during the invwarp process) was about 35min.
Is there any way to overcome this obvious drawback?
Thank you
Antonios Konstantinos
fslhd S01_LPI_ITKsnap_spm8_brain.nii.gz
filename S01_LPI_ITKsnap_spm8_brain.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 256
dim2 124
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 0.8593750000
pixdim2 1.5000000000
pixdim3 0.8593750000
pixdim4 0.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
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 Aligned Anat
qform_code 2
qto_xyz:1 0.859375 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 1.500000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 0.859375 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 Scanner Anat
sform_code 1
sto_xyz:1 0.859375 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 1.500000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.859375 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Left-to-Right
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL4.1
aux_file
fslstats S01_LPI_ITKsnap_spm8_brain.nii.gz -w
47 149 3 109 43 169 0 1
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