Hello FSLers,
I'm trying to do VBM in a set of 3D volumes acquired in sagittal but
converted to axial with fslswapdim, first thing I've tried is Bet with the
"Bias field & neck cleanup", because of the sagittal orientation. Anyway,
even if I wasn't trying to do VBM, the bias correction is not working for
me, the brain extraction is ok. I've tried with axial and sagittal
orientated volumes and the result is the same for both.
Any help would be appreciated
The command used by Bet is:
/usr/local/fsl/bin/bet
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain -B -f
0.35 -g 0
The output is:
Input image
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_unbiased
not valid
Error: input image
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_unbiased_premask
not valid
/usr/local/fsl/bin/bet: line 383: 5188 Segmentation fault
${FSLDIR}/bin/fast -oba 100 ${OUT}_tmp_premask >&/dev/null
** ERROR (nifti_image_read): failed to find header file for
'/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_premask_abias'
** ERROR:
nifti_image_open(/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_premask_abias):
bad header info
Error: failed to open file
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_premask_abias
ERROR: Could not open image
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_premask_abias
Image Exception : #22 :: Failed to read volume
/media/DATOS_E/MRI/P2369/P2369_FSL/3D/VBM/PAC_092157__3Daxial_brain_tmp_premask_abias
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/bet: line 383: 5195 Aborted
${FSLDIR}/bin/fslmaths $IN -mul ${OUT}_tmp_premask_abias ${OUT}_tmp_unbiased
Finished
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