Hi,

Did you mean that when you ran brain extraction on both images you saw the same quality of result?  Or were you just talking about the output of robustfov before running brain extraction?  All robustfov does is remove part of the image, so there should not be any differences in the latter.  However, if you are still having trouble with brain extraction after using robustfov correctly then it would indicate that the problem is not caused by the amount of neck in the image and you'll need to try other options (e.g. -f and -g and -R) to see if you can improve your BET results.

All the best,
Mark


From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Lili He <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, 13 August 2015 16:25
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] extra-Brain tissue "circled" in BET

I came across the same problem. I did specified file name for the output, while the neck was still there, no difference was noticed between input and output... Anything else am I missing?
Thank you,
Lili
On Thu, Aug 13, 2015 at 10:44 AM, paul mccarthy <[log in to unmask]> wrote:
Hi Hoifong,

You can use the '-r' option to robustfov to output a cropped version of the image, i.e.:

'robustfov -i input.nii.gz -r cropped_input.nii.gz'

Cheers,

Paul

On 13 August 2015 at 15:39, Chan Hoi Fong <[log in to unmask]> wrote:
Paul, 
   Is it correct to key robustfov -i "file name" ? however, it just shows

Final FOV is: 

0.000000 464.000000 154.000000 340.000000 0.000000 176.000000 

and i check the file with fslview, the neck is not removed. I thought i must miss some steps. 

thanks!

hoifong


On Wed, Aug 12, 2015 at 11:23 PM, paul mccarthy <[log in to unmask]> wrote:
Hi Hoifong,

BET can have trouble with images which have large amounts of neck - try using the 'robustfov' command to remove the neck area, and re-running BET.

Cheers,

Paul

On 12 August 2015 at 16:09, Chan Hoi Fong <[log in to unmask]> wrote:
​​I have upload the file to the Google drive, thanks!!​
 FM05_struc_to_FM05_struc_brain.png
​

On Wed, Aug 12, 2015 at 8:58 PM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

We recommend uploading illustrative pictures (not nifti files) to a third-party website (e.g. a photo sharing site) and including the link in emails to the list if you want to demonstrate something.  The limit is imposed to prevent people's inboxes being overwhelmed by people posting nifti files or other large attachments.

I'm afraid I can't really comment on how important the brain extraction errors are without seeing any images though.  What really matters is whether anything in the extra-brain regions gets segmented as grey matter or not.

All the best,
Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "subscribe FSL Hoi Fong, Chan" <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, 12 August 2015 02:11
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] extra-Brain tissue "circled" in BET

Dear Experts,
   I am doing VBM analysis currently . I have run fslreorient2std to reorient all sample. Then i run fslvbm_1_bet –N. However, there are several sampled showing much more extra-brain area circled as the post BET brain area. Will it affect the further analysis? ( i could not upload the image file since it is too large)
Thanks!!
hoifong




--
Hoi Fong, Chan, MD
En Chu Kong hospital, Department of neurology
National Taiwan University , Department of anatomy and cell biology
Taipei




--
Hoi Fong, Chan, MD
En Chu Kong hospital, Department of neurology
National Taiwan University , Department of anatomy and cell biology
Taipei