Hello all
I am getting an error when running SIENA between 2 scans of the same subject (FSL 4.1.2 on Linux Centos x64)
> export PRIORS="/usr/local/fsl-latest/data/standard/tissuepriors"
> siena mprage2006 mprage2007 -d -B "-f 0.4 -o -m" -m -S "-n 3 -b -g -B -P -A ${PRIORS}/avg152T1_gray ${PRIORS}/avg152T1_white ${PRIORS}/avg152T1_csf"
The error is:
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'B_halfwayto_A'
** ERROR: nifti_image_open(B_halfwayto_A): bad header info
Error: failed to open file B_halfwayto_A
ERROR: Could not open image B_halfwayto_A
Image Exception : #22 :: Failed to read volume B_halfwayto_A
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-latest/bin/siena: line 259: 6838 Aborted ${FSLDIR}/bin/overlay 1 0 -c ${B}_halfwayto_${A} -a ${B}_halfwayto_${A}_brain_seg 1.1 3 ${B}_halfwayto_${A}_brain_seg_grot
** ERROR (nifti_image_read): failed to find header file for 'B_halfwayto_A_brain_seg_grot'
** ERROR: nifti_image_open(B_halfwayto_A_brain_seg_grot): bad header info
Error: failed to open file B_halfwayto_A_brain_seg_grot
ERROR: Could not open image B_halfwayto_A_brain_seg_grot
Image Exception : #22 :: Failed to read volume B_halfwayto_A_brain_seg_grot
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-latest/bin/siena: line 260: 6839 Aborted ${FSLDIR}/bin/slicer ${B}_halfwayto_${A}_brain_seg_grot -a ${B}_halfwayto_${A}_brain_seg.png
** ERROR (nifti_image_read): failed to find header file for 'A_halfwayto_B'
** ERROR: nifti_image_open(A_halfwayto_B): bad header info
Error: failed to open file A_halfwayto_B
ERROR: Could not open image A_halfwayto_B
Image Exception : #22 :: Failed to read volume A_halfwayto_B
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-latest/bin/siena: line 265: 6866 Aborted ${FSLDIR}/bin/overlay 1 0 -c ${A}_halfwayto_${B} -a ${A}_halfwayto_${B}_brain_seg 1.1 3 ${A}_halfwayto_${B}_brain_seg_grot
** ERROR (nifti_image_read): failed to find header file for 'A_halfwayto_B_brain_seg_grot'
** ERROR: nifti_image_open(A_halfwayto_B_brain_seg_grot): bad header info
Error: failed to open file A_halfwayto_B_brain_seg_grot
ERROR: Could not open image A_halfwayto_B_brain_seg_grot
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg_grot
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-latest/bin/siena: line 266: 6867 Aborted ${FSLDIR}/bin/slicer ${A}_halfwayto_${B}_brain_seg_grot -a ${A}_halfwayto_${B}_brain_seg.png
dc: stack empty
dc: stack empty
** ERROR (nifti_image_read): failed to find header file for 'A_to_B_flow'
** ERROR: nifti_image_open(A_to_B_flow): bad header info
Error: failed to open file A_to_B_flow
Cannot open volume A_to_B_flow for reading!
** ERROR (nifti_image_read): failed to find header file for 'A_halfwayto_B'
** ERROR: nifti_image_open(A_halfwayto_B): bad header info
Error: failed to open file A_halfwayto_B
ERROR: Could not open image A_halfwayto_B
Image Exception : #22 :: Failed to read volume A_halfwayto_B
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-latest/bin/siena: line 276: 6902 Aborted ${FSLDIR}/bin/overlay 0 0 ${A}_halfwayto_${B} -a ${A}_to_${B}_flow 0.01 1 ${A}_to_${B}_flowneg 0.01 1 ${A}_halfwayto_${B}_render
** ERROR (nifti_image_read): failed to find header file for 'A_halfwayto_B_render'
** ERROR: nifti_image_open(A_halfwayto_B_render): bad header info
Error: failed to open file A_halfwayto_B_render
ERROR: Could not open image A_halfwayto_B_render
Image Exception : #22 :: Failed to read volume A_halfwayto_B_render
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl-latest/bin/siena: line 277: 6903 Aborted ${FSLDIR}/bin/slicer ${A}_halfwayto_${B}_render -s 1 -x 0.4 gr${A}_halfwayto_${B}a.png -x 0.5 gr${A}_halfwayto_${B}b.png -x 0.6 gr${A}_halfwayto_${B}c.png -y 0.4 gr${A}_halfwayto_${B}d.png -y 0.5 gr${A}_halfwayto_${B}e.png -y 0.6 gr${A}_halfwayto_${B}f.png -z 0.4 gr${A}_halfwayto_${B}g.png -z 0.5 gr${A}_halfwayto_${B}h.png -z 0.6 gr${A}_halfwayto_${B}i.png
Cannot open grA_halfwayto_Ba.png for reading
/usr/local/fsl-latest/bin/siena: line 278: 6904 Segmentation fault ${FSLDIR}/bin/pngappend gr${A}_halfwayto_${B}a.png + gr${A}_halfwayto_${B}b.png + gr${A}_halfwayto_${B}c.png + gr${A}_halfwayto_${B}d.png + gr${A}_halfwayto_${B}e.png + gr${A}_halfwayto_${B}f.png + gr${A}_halfwayto_${B}g.png + gr${A}_halfwayto_${B}h.png + gr${A}_halfwayto_${B}i.png ${A}_halfwayto_${B}_render.png
/bin/rm: cannot remove `grA_halfwayto_B?.???': No such file or directory
Finished. The SIENA report can be viewed by pointing your web browser at:
file:/home/evangeloui/data/mprage2006_to_mprage2007_siena/report.html
Estimated percentage brain volume change (PBVC) = 2.0
From the report I am missing the following images under :
FAST tissue segmentation
and
Final brain edge movement image
Thanks in advance
Iordanis
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Iordanis E. Evangelou, DPhil
Research Fellow
Neuroimaging Section
Neuroimmunology Branch
National Institute of Neurological Disorders and Stroke
National Institutes of Health
Building 10, Room 5C203B
Bethesda, MD 20892
USA
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