Dear Antonios,
what version of FSL are you using? As of FSL 5.0 we are using a different method for calculating the inverse and I hope/think that the problem you describe should no longer be there.
Jesper
On 4 Feb 2013, at 14:34, Antonios-Konstantinos Thanellas wrote:
> 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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