Dear Steve,
I wonder if label 0 in Talairach Daemon Lables means the whole brain? If so, hiding label 0 may be wrong, because some times we need to know which region elicits the highest activation at the whole brain level. So I suggest to check whether $fmri(atlaslabel) equals zero before calling fslmaths. Code is recommended as below:
replace line 444 in ${FSLDIR}/tcl/featquery.tcl with
========================================================================================================================================================================
if { $fmri(atlaslabel) == 0 } {
fsl:exec "${FSLDIR}/bin/fslmaths ${FSLDIR}/data/atlases/$atlasimage($fmri(atlasmask)) -thr $fmri(atlaslabel) -bin $fmri(mask)"
} else {
fsl:exec "${FSLDIR}/bin/fslmaths ${FSLDIR}/data/atlases/$atlasimage($fmri(atlasmask)) -thr $fmri(atlaslabel) -uthr $fmri(atlaslabel) -bin $fmri(mask)"
}
========================================================================================================================================================================
Best Regards
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Feng Xue
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡[log in to unmask]
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2009-03-04
National Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China. 100875
Tel: 86-13810154455(m)
Fax: 86-10-58806154(o)
web: http://psychbrain.bnu.edu.cn
============================================================
Welcome to MuDuo JinSheng BBS @ Beijing Normal University
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======= 2009-03-04 16:03:25 U wrote£º=======
>Hi - you're right that it won't correctly process these "0" labels for
>the label atlases - though that wouldn't make sense to select anyway
>as they correspond to the background.
>Thanks for pointing this out - I've amended Featquery so that it
>doesn't show the "0" label option for the labels atlases.
>Cheers.
>
>
>On 3 Mar 2009, at 10:51, Feng Xue wrote:
>
>> Dear folk,
>>
>> When using Talairach Daemon Lables or JHU ICBM-DTI-81 White-Matter
>> Lables as atlas in Featquery, Featquery will first call fslmaths to
>> generate a binary mask (command as below)
>> $FSLDIR/bin/fslmaths $FSLDIR/data/atlases//Talairach/Talairach-
>> labels-2mm -thr 1058 -uthr 1058 -bin /tmp/featquery_4VE87F
>> Mostly, it'll run as precise as we predict. But if we chose label 0
>> as our roi, there would be no valid mask, because of uthr = 0
>> (command as below)
>> $FSLDIR/bin/fslmaths $FSLDIR/data/atlases//Talairach/Talairach-
>> labels-2mm -thr 0 -uthr 0 -bin /tmp/featquery_4VE87F
>>
>> So I would suggest to judge atlas id first then call fslmaths in
>> $FSLDIR/tcl/featquery.tcl.
>>
>>
>> Best Regards
>>
>>
>> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Feng Xue
>> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡[log in to unmask]
>> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2009-03-03
>>
>> National Key Laboratory of Cognitive Neuroscience and Learning
>> Beijing Normal University
>> Beijing, China. 100875
>> Tel: 86-13810154455(m)
>> Fax: 86-10-58806154(o)
>> web: http://psychbrain.bnu.edu.cn
>> ============================================================
>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
>> telnet://bbs.mdjs.org
>> http://bbs.mdjs.org
>
>
>---------------------------------------------------------------------------
>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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