JISCMail - FSL Archives

Hi,

for those images that have not been skull-stripped properly, you can also try to directly run bet -R with the best -f option (that you have to determine empirically on your data, by default in FSL-VBM, it's 0.4) on your *_struc_cut.nii.gz, renaming the output of this process *_struc_brain.nii.gz.

Cheers,

Gwenaelle

------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
MRC Career Development Fellow
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
-----------------------------------------------------------------------------------------------

De : Rujing Zha <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Jeudi 24 octobre 2013 11h23
Objet : Re: [FSL] fslvbm_1_bet cannot strip skull and neck

Hi,

I didnot run that codes,and our fsl didnot has that codes. I donot know why.

Best.

2013-10-24

Rujing Zha

发件人：Mark Jenkinson <[log in to unmask]>

发送时间：2013-10-24 16:17

主题：Re: [FSL] fslvbm_1_bet cannot strip skull and neck

收件人："FSL"<[log in to unmask]>

抄送：

Hi,

Have you tried fsl_anat for brain extraction?

All the best,

Mark

On 23 Oct 2013, at 16:36, Rujing Zha <[log in to unmask]> wrote:

Hi Gwenaëlle,
This -R cannot strip the bottom left of brain images.What else can I do?

Any advice will be appreciated!

Thanks!

Rujing Zha

在 2013-10-15 19:34:14，"Gwenaëlle DOUAUD" <[log in to unmask]> 写道：

Hi Rujing,

thanks. Maybe try with: fslvbm_1_bet -N -R?

and let us know if this helps.

Cheers,
Gwenaëlle

------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
-----------------------------------------------------------------------------------------------

De : Rujing Zha <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Mardi 15 octobre 2013 12h04
Objet : Re: [FSL] fslvbm_1_bet cannot strip skull and neck

Hi,

yes! two pictures were attached here.

thanks.

Best.

rujing

At 2013-10-15 18:26:48,"Gwenaëlle DOUAUD" <[log in to unmask]> wrote:

Hi,

so you have run the same command for all subjects? It would be useful if you could attach an example (low resolution snapshot) of one subject on which the process worked well and one on which it didn't.

Cheers,

Gwenaëlle

------------------------------------------------------------------------------------------------
Gwenaëlle Douaud, PhD
MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
-----------------------------------------------------------------------------------------------

De : Rujing Zha <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Mardi 15 octobre 2013 3h32
Objet : [FSL] fslvbm_1_bet cannot strip skull and neck

Hi all,
when i run fslvbm_1_bet -N, some subjects can extract brain volumn.however some subjects cannot strip neck and skull.

what should i do?

any reply will be appreciated.

best.

rujing zha