Hi, I guess you want to change the lines:
${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -
thr 4.5 -bin ${I}_tmpmask
${FSLDIR}/bin/flirt -in ${I}_tmpmask -ref ${I}_brain -out $
{I}_stdmask_segvent -applyxfm -init ${I}2std_inv.mat
${FSLDIR}/bin/avwmaths ${I}_stdmask_segvent -thr 0.5 -bin $
{I}_stdmask_segvent
to:
${FSLDIR}/bin/flirt -in <YOURMASK> -ref ${I}_brain -out $
{I}_stdmask_segvent -applyxfm -init ${I}2std_inv.mat
${FSLDIR}/bin/avwmaths ${I}_stdmask_segvent -thr 0.5 -bin $
{I}_stdmask_segvent
/bin/rm ${I}_tmpmask*
Cheers.
On 4 Dec 2007, at 18:17, Paul Geha wrote:
> Dear FSL users,
>
> I am trying to get the lateral ventricle volumes using Sienax. I
> just need the volume of these two ventricles. I constructed a
> standard space mask for them and I am planning to replace one of
> the Standard masks ( in fsl/etc/standard/) of fsl-3.3.2 with mine to
> get the output I need . Can you please tell me which one to replace
> to get the output in t1.sienax?
> thanks a lot
> Paul
>
>
>
>
> Paul Geha M.D.
> Northwestern University
> The Feinberg School of Medicine
> Department of Physiology M211
> 303 E. Chicago Ave.
> Chicago, IL 60611
> Tel:312-503 2886
> Fax: 312-503-5101
>
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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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