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FSL  November 2007

FSL November 2007

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Subject:

RE : [FSL] another registration problem

From:

Gwenaëlle DOUAUD <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sat, 3 Nov 2007 02:30:54 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (166 lines)

Hi Naama,

then, you might give a try with the -t (not -T) option
in tbss_2_reg. This allows you to specify an
alternative target to the "best" one and the standard
template... Another scan of one of the kid should do
the trick.

Hope this helps,
Gwenaëlle


--- Naama Barnea-Goraly <[log in to unmask]> a écrit
:

> 
> Yes all of my images generated from tbss_3 get
> tilted like that not  
> just one, but this is because my target image is the
> problem. My  
> target image doesn't register well to the MNI
> template. Even when I  
> flirt the target image to MNI space it gets tilted.
> Unfortunately I  
> cannot use the -T option because my subjects are all
> young kids. The  
> other images flirt just fine.
> 
> Thank for your help,
> 
> Naama
> 
> 
> 
> On Nov 1, 2007, at 5:52 AM, Gwenaëlle DOUAUD wrote:
> 
> > Hi Naama,
> >
> > you have not given much information so, from what
> I
> > can see (#713049), I assume that the non-linear
> > registration of one of the FA map has failed when
> > running tbss_3, or do all your images appear
> distorted
> > in a similar way?
> > If they are all like that, I would suggest
> re-running
> > tbss_2 with the -T option (recommended anyway)...
> > If this is only the case for one FA map, it may be
> > because the affine initialisation has failed. In
> this
> > case, just quickly flirt the image to the best
> target
> > and then run areg and nreg on it (see previous
> emails
> > to see the usage).
> >
> > Hope this helps,
> > Gwenaelle
> >
> > PS: Next time, please send your email on the FSL
> > mailing list and not at a personal address :-)
> >
> >
> > --- Naama Barnea-Goraly <[log in to unmask]> a
> écrit
> > :
> >
> >>
> >>
> >> I am trying to get my dataset to work with tbss
> 1.1
> >> (fsl4). But when
> >> I run tbss_2 and then tbss_3 I get the following
> >> image (tilted). I am
> >> using the -n option in tbss_2
> >>
> >> Thanks again for your help,
> >>
> >> Naama
> >>
> >>
> >> 
> >>
> >>
> >>
> >> CONFIDENTIALITY NOTICE:  This e-mail
> communication
> >> and any
> >> attachments may contain confidential information
> for
> >> the use of the
> >> designated recipients named above.  If you are
> not
> >> the intended
> >> recipient, you are hereby notified that you have
> >> received this
> >> communication in error and that any review,
> >> disclosure,
> >> dissemination, distribution or copying of it or
> its
> >> contents is
> >> prohibited.  If you have received this
> communication
> >> in error, please
> >> notify Stanford Medical Center immediately by
> >> telephone at (650)
> >> 725-5722 and destroy all copies of this
> >> communication and any
> >> attachments.  Thank you.
> >>
> >>
> >>
> >
> >
> >
> >        
> >
>
______________________________________________________________________
> 
> > _______
> > Ne gardez plus qu'une seule adresse mail ! Copiez
> vos mails vers  
> > Yahoo! Mail
> 
> 
> Naama Barnea-Goraly M.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University Division of Child and Adolescent
> Psychiatry
> 401 Quarry Rd. MC 5795
> Stanford University School of Medicine
> Stanford, CA  94305-5795
> fax:     (650) 724-4794
> Phone: (650) 724-3779
> 
> 
> CONFIDENTIALITY NOTICE:  This e-mail communication
> and any  
> attachments may contain confidential information for
> the use of the  
> designated recipients named above.  If you are not
> the intended  
> recipient, you are hereby notified that you have
> received this  
> communication in error and that any review,
> disclosure,  
> dissemination, distribution or copying of it or its
> contents is  
> prohibited.  If you have received this communication
> in error, please  
> notify Stanford Medical Center immediately by
> telephone at (650)  
> 725-5722 and destroy all copies of this
> communication and any  
> attachments.  Thank you.
> 
> 
> 



      _____________________________________________________________________________ 
Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail 

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