Dear fsl users
i changed siena script in order to combine betpremasking and then robust
brain extraction on the betpremasked image. The changes i've done are the
following :
echo "---------- extract brain
--------------------------------------------" >> report.siena
${FSLDIR}/bin/bet $A ${A}_brain -R -s -m >> report.siena
${FSLDIR}/bin/standard_space_roi $A ${A}_brain_tmp -b -d
${FSLDIR}/bin/bet ${A}_brain_tmp ${A}_brain -R -f 0.2 -g 0 -m
${FSLDIR}/bin/bet $B ${B}_brain -R -s -m >> report.siena
${FSLDIR}/bin/standard_space_roi $B ${B}_brain_tmp -b -d
${FSLDIR}/bin/bet ${B}_brain_tmp ${B}_brain -R -f 0.2 -g 0 -m
Though when i run the script : siena input output -d
I have the following errors that are attached to this email
Do you have an idea on how to solve this problem?
Thank you
Antonios-Constantine Thanellas
On Sat, 27 Oct 2007 10:48:57 +0100, Steve Smith <[log in to unmask]> wrote:
>Hi,
>
>If you want more complex BET calls (e.g. standard_space_roi as well
>as BET robust etc) then you can just take a local copy of $FSLDIR/bin/
>siena and edit the two BET lines near the top, putting in whatever
>you need. Don't forget though to make sure you generate the skull
>images as well as the brain and brain mask images.
>
>Cheers, Steve.
>
>
>On 26 Oct 2007, at 00:26, Antonios - Constantine Thanellas wrote:
>
>> Hi Steve,
>>
>> I've tried the -B option inside siena ( -B "-B") though in this case
>> automatically i exclude bet_robust choice from siena. There's no
>> way to feed
>> siena with the image that comes from betrobust segmentation of the
>> betpremasked image? I am asking that because when i applied
>> betrobust on an
>> image which was first betpremasked i had excellent brain segmentation
>> results and i hope that the same would happen if i could manage to
>> combine
>> both of the tools in siena
>>
>> When i used -B "-B" option on siena even though the bet results
>> were decent
>> (but definitely not as good as the results that i had using
>> betrobust on the
>> betpremasked image) and i thought that my problem was solved, i
>> noticed that
>> the halfway tranformations on both images were totally wrong
>> containing all
>> the neck... why this happened since bet extraction was done
>> successfully in
>> siena?What do you suggest to do in this case?
>>
>> I've uploaded the png files that shows the different stages of
>> siena (which
>> failed) on the A and B images with the ref number: 625404
>>
>> Thanks again Steve
>> Antonios-Constantine Thanellas
>>
>>
>>
>> On Thu, 25 Oct 2007 07:42:33 +0100, Steve Smith
>> <[log in to unmask]> wrote:
>>
>>> Have you tried the -B option to bet? You can pass that into SIENA by
>>> adding onto the end of the SIENA command
>>> -B "-B"
>>> Cheers.
>>>
>>>
>>> On 24 Oct 2007, at 20:52, Antonios - Constantine Thanellas wrote:
>>>
>>>> Dear fsl users
>>>>
>>>> I want to betpremask (through standard_space_roi) my data in order
>>>> to do
>>>> longitudinal and cross sectional analysis with siena and sienax
>>>> respectively.
>>>>
>>>> Since siena needs the skulls of the original images i can't just do
>>>> a shell
>>>> script that sends as inputs to siena the stripped brain images after
>>>> betpremasking them. I've read in FSL forum that it's better to
>>>> change the
>>>> siena script as follows: "leave BET to extract the skulls, then run
>>>> betpremask and feed, then run again bet on the premasked images and
>>>> feed
>>>> siena with these results." The problem is that siena script is too
>>>> complicated for my scripting skills and i would really appreciate
>>>> if you
>>>> could tell me how to change this script in order to betpremask my
>>>> data first
>>>> (bet_robust totally fails in most of my data which contain big
>>>> protions of
>>>> neck even if i determine the COG with the -c option.That's why i
>>>> need
>>>> betpremask since it gives me really good results).I use the fsl 4.0
>>>> version
>>>> on ubuntu platform.
>>>>
>>>> How about sienax ? it also needs the skulls in order to register
>>>> the images
>>>> with pairreg? How the sienax script should be changed in order to
>>>> incorporate betpremasking?In this case also, a shell script that
>>>> sends as
>>>> inputs to sienax the betpremasked images wouldn't work..Right?
>>>>
>>>> Thank's a lot for your time
>>>>
>>>> Antonios-Constantine Thanellas
>>>
>>>
>>> ---------------------------------------------------------------------
>>> ---
>>> ---
>>> 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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** ERROR (nifti_image_read): failed to find header file for 'B_halfwayto_A_brain_seg'
** ERROR: nifti_image_open(B_halfwayto_A_brain_seg): bad header info
Error: failed to open file B_halfwayto_A_brain_seg
ERROR: Could not open image B_halfwayto_A_brain_seg
Image Exception : #22 :: Failed to read volume B_halfwayto_A_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/siena_with_bet_robust: line 268: 20821 Aborted (core dumped) ${FSLDIR}/bin/siena_diff ${B} ${A} -c $corr $sdo $sdopts >> report.siena
** ERROR (nifti_image_read): failed to find header file for 'B_halfwayto_A_brain_seg'
** ERROR: nifti_image_open(B_halfwayto_A_brain_seg): bad header info
Error: failed to open file B_halfwayto_A_brain_seg
ERROR: Could not open image B_halfwayto_A_brain_seg
Image Exception : #22 :: Failed to read volume B_halfwayto_A_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/siena_with_bet_robust: line 270: 21015 Aborted (core dumped) ${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/lib/fsl/siena_with_bet_robust: line 271: 21018 Aborted (core dumped) ${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_brain_seg'
** ERROR: nifti_image_open(A_halfwayto_B_brain_seg): bad header info
Error: failed to open file A_halfwayto_B_brain_seg
ERROR: Could not open image A_halfwayto_B_brain_seg
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/siena_with_bet_robust: line 275: 21046 Aborted (core dumped) ${FSLDIR}/bin/siena_diff ${A} ${B} -c $corr $sdo $sdopts >> report.siena
** ERROR (nifti_image_read): failed to find header file for 'A_halfwayto_B_brain_seg'
** ERROR: nifti_image_open(A_halfwayto_B_brain_seg): bad header info
Error: failed to open file A_halfwayto_B_brain_seg
ERROR: Could not open image A_halfwayto_B_brain_seg
Image Exception : #22 :: Failed to read volume A_halfwayto_B_brain_seg
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/siena_with_bet_robust: line 276: 21234 Aborted (core dumped) ${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/lib/fsl/siena_with_bet_robust: line 277: 21239 Aborted (core dumped) ${FSLDIR}/bin/slicer ${A}_halfwayto_${B}_brain_seg_grot -a ${A}_halfwayto_${B}_brain_seg.png
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** 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_to_B_flow'
** ERROR: nifti_image_open(A_to_B_flow): bad header info
Error: failed to open file A_to_B_flow
ERROR: Could not open image A_to_B_flow
Image Exception : #22 :: Failed to read volume A_to_B_flow
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/lib/fsl/siena_with_bet_robust: line 287: 21276 Aborted (core dumped) ${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/lib/fsl/siena_with_bet_robust: line 288: 21279 Aborted (core dumped) ${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/lib/fsl/siena_with_bet_robust: line 289: 21282 Segmentation fault (core dumped) ${FSLDIR}/bin/pngappend gr${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/dinos/Desktop/testaki_gia_siena/testaki_siena_with_script_standard_space_roi/002_S_0938_AD_sc_to_Desktop/testaki_gia_siena/testaki_siena_with_script_standard_space_roi/002_S_0938_AD_m06_siena/report.html
Estimated percentage brain volume change (PBVC) =
2.0
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