Thanks Steve
I am actually including it as capital -S. does it matter in which order I include it?
when I run sienax they work with no errors
sienax mprage -B "-f 0.4 -o -m" -S "-n 3 -b -g -B -P -A ${PRIORS}/avg152T1_gray ${PRIORS}/avg152T1_white ${PRIORS}/avg152T1_csf" -d
Iordanis
-------------------------------------------------------------------
Iordanis E. Evangelou, DPhil, Eur Ing, MIET
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
-------------------------------------------------------------------
" If we knew what it was we were doing, it would not be called research, would it? "
Albert Einstein
-----Original Message-----
From: Steve Smith [mailto:[log in to unmask]]
Sent: Thursday, January 29, 2009 3:40 AM
To: [log in to unmask]
Subject: Re: [FSL] SIENA Error
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
>
> -------------------------------------------------------------------
>
>
>
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|