Hi - no, that's not quite right. In your call to siena you correctly
specify -S in order to pass the following options in quotes to
siena_diff, i.e. you are passing on to siena_diff:
-n 3 -b -g -B -P -A ${PRIORS}/avg152T1_gray ${PRIORS}/avg152T1_white $
{PRIORS}/avg152T1_csf
Now, I assume that you want siena_diff to pass these options on to
fast, so, looking at the siena_diff options, you need to precede all
of these with -s. Hence your original call should be
siena mprage2006 mprage2007 -d -B "-f 0.4 -o -m" -m -S "-s -n 3 -b -g -
B -P -A ${PRIORS}/avg152T1_gray ${PRIORS}/avg152T1_white ${PRIORS}/
avg152T1_csf"
Cheers.
On 29 Jan 2009, at 17:02, Evangelou, Iordanis (NIH/NINDS) [E] wrote:
> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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