Hi - you need to run standard_space_roi first - as this stands, your
skull images will have the wrong dimensions.
Cheers.
On 31 Oct 2007, at 15:19, Antonios - Constantine Thanellas wrote:
> 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
>> ------------------------------------------------------------------------
>> ---
>> =
>> =
>> =
>> =
>> =====================================================================
>
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> dc: stack empty
> ** 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
> 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_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
>
>
>
---------------------------------------------------------------------------
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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