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I am trying to run sienax module on T1 dataset. But it shows me following error. The volume for all segmentations is same which is obviously wrong. Any help will be appreciated.
/usr/local/fsl/bin/sienax: line 285: 6897 Aborted ${FSLDIR}/bin/fast -g $imtype $segopts ${I}_stdmaskbrain >> report.sienax 2>&1
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1
Cannot open volume I_stdmaskbrain_pve_1 for reading!
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1_segperiph'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1_segperiph): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1_segperiph
ERROR: Could not open image I_stdmaskbrain_pve_1_segperiph
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1_segperiph
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_0'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_0): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_0
Cannot open volume I_stdmaskbrain_pve_0 for reading!
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_0_segvent'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_0_segvent): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_0_segvent
ERROR: Could not open image I_stdmaskbrain_pve_0_segvent
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_0_segvent
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1
ERROR: Could not open image I_stdmaskbrain_pve_1
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_2'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_2): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_2
ERROR: Could not open image I_stdmaskbrain_pve_2
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_2
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_seg'
** ERROR: nifti_image_open(I_stdmaskbrain_seg): bad header info
ERROR: failed to open file I_stdmaskbrain_seg
ERROR: Could not open image I_stdmaskbrain_seg
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 289: 6975 Aborted ${FSLDIR}/bin/overlay 1 1 -c ${I} -a ${I}_stdmaskbrain_seg 1.9 5 ${I}_render
** ERROR (nifti_image_read): failed to find header file for 'I_render'
** ERROR: nifti_image_open(I_render): bad header info
ERROR: failed to open file I_render
ERROR: Could not open image I_render
Image Exception : #22 :: Failed to read volume I_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 290: 6979 Aborted ${FSLDIR}/bin/slicer ${I}_render -s 1 -x 0.4 gr${I}a.png -x 0.5 gr${I}b.png -x 0.6 gr${I}c.png -y 0.4 gr${I}d.png -y 0.5 gr${I}e.png -y 0.6 gr${I}f.png -z 0.4 gr${I}g.png -z 0.5 gr${I}h.png -z 0.6 gr${I}i.png
Cannot open grIa.png for reading
/usr/local/fsl/bin/sienax: line 291: 6980 Segmentation fault ${FSLDIR}/bin/pngappend gr${I}a.png + gr${I}b.png + gr${I}c.png + gr${I}d.png + gr${I}e.png + gr${I}f.png + gr${I}g.png + gr${I}h.png + gr${I}i.png ${I}_render.png
/bin/rm: cannot remove `grI?.???': No such file or directory
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_1_segperiph'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_1_segperiph): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_1_segperiph
ERROR: Could not open image I_stdmaskbrain_pve_1_segperiph
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_1_segperiph
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 305: 6982 Aborted ${FSLDIR}/bin/overlay 0 1 -c ${I} -a ${I}_stdmaskbrain_pve_1_segperiph 0.3 0.7 ${I}_periph_render
** ERROR (nifti_image_read): failed to find header file for 'I_stdmaskbrain_pve_0_segvent'
** ERROR: nifti_image_open(I_stdmaskbrain_pve_0_segvent): bad header info
ERROR: failed to open file I_stdmaskbrain_pve_0_segvent
ERROR: Could not open image I_stdmaskbrain_pve_0_segvent
Image Exception : #22 :: Failed to read volume I_stdmaskbrain_pve_0_segvent
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 305: 6986 Aborted ${FSLDIR}/bin/overlay 0 1 -c ${I} -a ${I}_stdmaskbrain_pve_0_segvent 0.3 0.7 ${I}_vent_render
** ERROR (nifti_image_read): failed to find header file for 'I_periph_render'
** ERROR: nifti_image_open(I_periph_render): bad header info
ERROR: failed to open file I_periph_render
ERROR: Could not open image I_periph_render
Image Exception : #22 :: Failed to read volume I_periph_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 305: 6989 Aborted ${FSLDIR}/bin/slicer ${I}_periph_render -s 1 -x 0.4 gr${I}a.png -x 0.5 gr${I}b.png -x 0.6 gr${I}c.png -y 0.4 gr${I}d.png -y 0.5 gr${I}e.png -y 0.6 gr${I}f.png -z 0.4 gr${I}g.png -z 0.5 gr${I}h.png -z 0.6 gr${I}i.png
Cannot open grIa.png for reading
/usr/local/fsl/bin/sienax: line 305: 6990 Segmentation fault ${FSLDIR}/bin/pngappend gr${I}a.png + gr${I}b.png + gr${I}c.png + gr${I}d.png + gr${I}e.png + gr${I}f.png + gr${I}g.png + gr${I}h.png + gr${I}i.png ${I}_periph_render.png
** ERROR (nifti_image_read): failed to find header file for 'I_vent_render'
** ERROR: nifti_image_open(I_vent_render): bad header info
ERROR: failed to open file I_vent_render
ERROR: Could not open image I_vent_render
Image Exception : #22 :: Failed to read volume I_vent_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/sienax: line 305: 6991 Aborted ${FSLDIR}/bin/slicer ${I}_vent_render -s 1 -x 0.4 gr${I}a.png -x 0.5 gr${I}b.png -x 0.6 gr${I}c.png -y 0.4 gr${I}d.png -y 0.5 gr${I}e.png -y 0.6 gr${I}f.png -z 0.4 gr${I}g.png -z 0.5 gr${I}h.png -z 0.6 gr${I}i.png
Cannot open grIa.png for reading
/usr/local/fsl/bin/sienax: line 305: 6992 Segmentation fault ${FSLDIR}/bin/pngappend gr${I}a.png + gr${I}b.png + gr${I}c.png + gr${I}d.png + gr${I}e.png + gr${I}f.png + gr${I}g.png + gr${I}h.png + gr${I}i.png ${I}_vent_render.png
/bin/rm: cannot remove `grI?.???': No such file or directory
Finished. The SIENAX report can be viewed by pointing your web browser at:
file:/media/disk/NFL_1mm_img/NFL_01_sienax/report.html
Estimated normalised brain volume (NBV) =
1.30
Thank you.
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