where can I get the sienax scripts?
b/w
Andres Roman Urrestarazu MD, MSc IHP, BM
University of Cambridge
Department of Psychiatry
Addenbrookes Hospital
Box 189
Cambridge
CB2 0QQ
UK
Telephone: 0044 01223 764421
Mobile: 0044 07 775614709
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Stephen Smith
Sent: Wed 3/3/2010 5:00 PM
To: [log in to unmask]
Subject: Re: [FSL] FSL total brain volume calculation
Hi - sure, have a look inside the sienax script to see how this does
these things.
Cheers.
On 3 Mar 2010, at 16:54, Andres Roman Urrestarazu wrote:
> Hi,
>
> Im trying to calculate total brain volume on fsl and I thinking of
> using SIENA. The pipeline that it uses involves skull stripping the
> images, segmenting and registering all jobs I have already done. Is
> there any way to skip this and get total brain volumes without going
> again over all this steps?
>
> Thank you very much again.
>
>
> best wishes
>
> Andres Roman Urrestarazu MD, MSc IHP, BM
>
> University of Cambridge
> Department of Psychiatry
> Addenbrookes Hospital
> Box 189
> Cambridge
> CB2 0QQ
> UK
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
> Sent: Mon 3/1/2010 3:20 PM
> To: [log in to unmask]
> Subject: Re: [FSL] design matrix
>
> You just need to change the number of inputs from 100 to 222.
>
> Cheers,
> Gwenaelle
>
> --- En date de : Lun 1.3.10, Andres Roman Urrestarazu
> <[log in to unmask]> a écrit :
>
> > De: Andres Roman Urrestarazu <[log in to unmask]>
> > Objet: Re: [FSL] design matrix
> > À: [log in to unmask]
> > Date: Lundi 1 mars 2010, 15h08
> >
> >
> >
> >
> >
> > RE: [FSL] design matrix
> >
> >
> >
> >
> > Hi again Gwenaelle,
> >
> >
> >
> > I did what you told me and I still have the issue that the
> > maximum amount of subjects that the Glm FSL GUI allows for
> > the design matrix is 100, and as I told you before I have
> > 222 in total. Is there anyway to get around this issue?
> > Thank you again for your help.
> >
> >
> >
> > Best wishes.
> >
> >
> >
> >
> >
> >
> >
> > Andres Roman Urrestarazu MD, MSc IHP, BM
> >
> >
> >
> > University of Cambridge
> >
> > Department of Psychiatry
> >
> > Addenbrookes Hospital
> >
> > Box 189
> >
> > Cambridge
> >
> > CB2 0QQ
> >
> > UK
> >
> > Telephone: 0044 01223 764421
> >
> > Mobile: 0044 07 775614709
> >
> >
> >
> >
> >
> >
> >
> > -----Original Message-----
> >
> > From: FSL - FMRIB's Software Library on behalf of
> > Gwenaëlle DOUAUD
> >
> > Sent: Fri 2/26/2010 4:30 PM
> >
> > To: [log in to unmask]
> >
> > Subject: Re: [FSL] design matrix
> >
> >
> >
> > Hi,
> >
> >
> >
> > exactly in the same way: specify in the "General
> > Linear Model" window that you have 4+3=7 evs in your
> > design matrix, with the first 4 columns being your 4 groups,
> > the next three your 3 covariates...
> >
> >
> >
> > Cheers,
> >
> > Gwenaelle
> >
> >
> >
> >
> >
> > --- En date de : Ven 26.2.10, Andres Roman Urrestarazu
> > <[log in to unmask]> a écrit :
> >
> >
> >
> > > De: Andres Roman Urrestarazu <[log in to unmask]>
> >
> > > Objet: Re: [FSL] design matrix
> >
> > > À: [log in to unmask]
> >
> > > Date: Vendredi 26 février 2010, 16h02
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > RE: [FSL]design matrix
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > Hi Gwenaelle,
> >
> > >
> >
> > >
> >
> > >
> >
> > > Thank you very much for your help. I still have some
> >
> > > questions regarding the design matrix for fslvbm.
> > Since as
> >
> > > you know I have four groups how can I add 3 different
> >
> > > covariates to my design matrix?
> >
> > >
> >
> > >
> >
> > >
> >
> > > Thank you again.
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > Andres Roman Urrestarazu MD, MSc IHP, BM
> >
> > >
> >
> > >
> >
> > >
> >
> > > University of Cambridge
> >
> > >
> >
> > > Department of Psychiatry
> >
> > >
> >
> > > Addenbrookes Hospital
> >
> > >
> >
> > > Box 189
> >
> > >
> >
> > > Cambridge
> >
> > >
> >
> > > CB2 0QQ
> >
> > >
> >
> > > UK
> >
> > >
> >
> > > Telephone: 0044 01223 764421
> >
> > >
> >
> > > Mobile: 0044 07 775614709
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > -----Original Message-----
> >
> > >
> >
> > > From: FSL - FMRIB's Software Library on behalf of
> >
> > > Gwenaëlle DOUAUD
> >
> > >
> >
> > > Sent: Tue 2/23/2010 5:22 PM
> >
> > >
> >
> > > To: [log in to unmask]
> >
> > >
> >
> > > Subject: Re: [FSL] fslvbm problems header
> >
> > >
> >
> > >
> >
> > >
> >
> > > Hi Andres,
> >
> > >
> >
> > >
> >
> > >
> >
> > > using the Glm gui, you simply need to specify in the
> >
> > > "General Linear Model" window that you have
> > 4 evs
> >
> > > in your design matrix (after switching from
> > timeseries
> >
> > > design to higher-level/non timeseries design in the
> >
> > > "GLM setup" window).
> >
> > >
> >
> > >
> >
> > >
> >
> > > Cheers,
> >
> > >
> >
> > > Gwenaelle
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > > Hi,
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > Im working on a big data sample (n=222) doing VBM
> > for
> >
> > >
> >
> > > > subjects at high risk of psychosis. I have come
> > across
> >
> > > some
> >
> > >
> >
> > > > issues with the design.mat since I have 4
> > different
> >
> > > groups
> >
> > >
> >
> > > > (Psychosis, clinical high risk, genetic risk and
> >
> > > controls)
> >
> > >
> >
> > > > comparing grey matter density between them. The
> > Glm
> >
> > > options
> >
> > >
> >
> > > > and FEAT usually involve a two group comparison
> > so I
> >
> > > was
> >
> > >
> >
> > > > wondering if any of you had any experience in
> > multiple
> >
> > > group
> >
> > >
> >
> > > > comparisons while creating the design matrix.
> > Thank
> >
> > > you very
> >
> > >
> >
> > > > much for your help.
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > best wishes
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > Andres Roman Urrestarazu MD, MSc IHP, BM
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > University of Cambridge
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > Department of Psychiatry
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > Addenbrookes Hospital
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > Box 189
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > Cambridge
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > CB2 0QQ
> >
> > >
> >
> > > >
> >
> > >
> >
> > > > UK
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > > >
> >
> > >
> >
> > >
> >
> > >
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> > >
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> > >
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> > >
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> > >
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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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