Thank you very much Steve,
I used the "-r" option but my problem is that for this subject I have in the sienax report a GM Volume smaller than the WM one which according to the literature is wrong.
Do you know what I should do to obtain the right proportion?
Thanks again,
Donatello
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith
Sent: Wednesday, April 01, 2009 7:19 AM
To: [log in to unmask]
Subject: Re: [FSL] Re : sienax
HI - I'd recommend having a look at the SIENA/SIENAX manual, at:
http://fsl.fmrib.ox.ac.uk/fsl/siena/
You can find various images output in the .sienax output directory - I
suggest having a look through these to see what it's outputting - make
sure you use the "-r" option if you want to get the peripheral cortex
GM volume and ventricular CSF volume maps.
Cheers, Steve.
On 1 Apr 2009, at 00:19, Arienzo, Donatello wrote:
> Hi,
> I am a new user of FSL.
> I used sienax to estimate the total brain tissue volume from a T1
> image. When I use fslview to look at the render file, is it possible
> to see the results for white matter and gray matter separately and
> not only the whole brain?
> Thanks,
>
> Donatello
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Gwenaëlle DOUAUD
> Sent: Tuesday, March 24, 2009 6:34 AM
> To: [log in to unmask]
> Subject: [FSL] Re : [FSL] Q:VBM analysis
>
> Hi Moran,
>
> for the VBM-WM analysis, please look for "vbm white matter" in the
> FSL archives: https://www.jiscmail.ac.uk/cgi-bin/webadmin?S1=fsl
>
> As for the children VBM analysis, it might be worth trying the
> standard FSL-VBM approach, as the only step to place the scans in
> the MNI space involving adult brains is an *affine* registration
> between your native GM images and the MNI 152 GM template. Then,
> with these affinely registered GM images, FSL-VBM creates a study-
> specific GM template, so a template that would be built *only* with
> the GM of young children involved in your analysis. Alternatively,
> you can have a look at the archives, typing "vbm children" as
> keywords...
>
> Hope this helps,
> Gwenaelle
>
>
> --- En date de : Mar 24.3.09, Moran Artzi <[log in to unmask]> a
> écrit :
>
>> De: Moran Artzi <[log in to unmask]>
>> Objet: [FSL] Q:VBM analysis
>> À: [log in to unmask]
>> Date: Mardi 24 Mars 2009, 6h20
>> Hi,
>> We previously successfully used the fsl_VBM analysis and
>> have 2 questions
>> regarding to our further analysis:
>> First- Can we use fsl_VBM analysis to study structural WM
>> differences?
>> In addition we intend to implement this analysis on group
>> of young children's
>> (~4 yo), is there adapted templates for this and other non-
>> adults study
>> groups?
>>
>> Many thanks
>> Moran
>
>
>
>
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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)
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