It looks like you're trying to pass options to fast in the siena_diff
options part, but you haven't including the "-s" at the start of that
final brackted list?
Cheers.
On 28 Jan 2009, at 22:54, Evangelou, Iordanis (NIH/NINDS) [E] wrote:
> 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
>
> -------------------------------------------------------------------
>
> 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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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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