Hi,

Difficult to say just from that. If you can make sub_2_t0.vol.nii.gz sub_2_t1.vol.nii.gz available, I'm happy to take a look for you. 

On Wednesday, October 26, 2016, Nabin Koirala <[log in to unmask]> wrote:

Dear FSL group,

I am trying to run SIENA for obtaining PBVC in a longitudinal scan but got this error. The command I am using is as shown below, and I have tried changing bet options and others too, using or not using standard mask and so on (as seeing the past queries in the forum) but still the error persists. I think it is also important to mention that the error is only for few subjects in the whole cohort. Your suggestions would be greatly appreciated.

command used:

siena sub_2_t0.vol.nii.gz sub_2_t1.vol.nii.gz -o sub_2_t0_t1 -B " -f 0.4"

And the output is as follows:

The output (if any) follows:

Running SIENA
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
dc: stack empty
Image Exception : #22 :: ERROR: Could not open image B_halfwayto_A_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/gpfs/fs1/home/nkoirala/fsl/bin/siena: line 281: 12745 Aborted                 ${FSLDIR}/bin/siena_diff ${B} ${A} -c $corr $sdo $sdopts >> report.siena
Image Exception : #22 :: ERROR: Could not open image B_halfwayto_A_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/gpfs/fs1/home/nkoirala/fsl/bin/siena: line 283: 12927 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
Image Exception : #22 :: ERROR: Could not open image B_halfwayto_A_brain_seg_grot
Error in slicer input, exiting...
Image Exception : #22 :: ERROR: Could not open image A_halfwayto_B_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/gpfs/fs1/home/nkoirala/fsl/bin/siena: line 288: 12954 Aborted                 ${FSLDIR}/bin/siena_diff ${A} ${B} -c $corr $sdo $sdopts >> report.siena
Image Exception : #22 :: ERROR: Could not open image A_halfwayto_B_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/gpfs/fs1/home/nkoirala/fsl/bin/siena: line 289: 13133 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
Image Exception : #22 :: ERROR: Could not open image A_halfwayto_B_brain_seg_grot
Error in slicer input, exiting...
dc: stack empty
dc: stack empty
Cannot open volume A_to_B_flow for reading!
Image Exception : #22 :: ERROR: Could not open image A_to_B_flow
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/gpfs/fs1/home/nkoirala/fsl/bin/siena: line 300: 13169 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
Image Exception : #22 :: ERROR: Could not open image A_halfwayto_B_render
Error in slicer input, exiting...

 Cannot open grA_halfwayto_Ba.png for reading
/gpfs/fs1/home/nkoirala/fsl/bin/siena: line 302: 13171 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:/gpfs/fs2/project/jgu-bestust/siena_output_92_sub/sub_13_t0_t1/report.html
Estimated percentage brain volume change (PBVC) =
2.0

Many thanks in advance.

Best,
Nabin

--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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