I think I got it. Melodic GUI never use bet, instead, it uses betfunc in pre-processing step. Or, I can choose command line function to do some 'liberal' analysis.
Thank you.
Dear Christian,
Thank you. but some further doubts induced from your reply...
(1)
when you use the GUI instead of the command
line then betfunc is
already used to find the mask which is then being passed to the
melodic binary
: ...thus melodic is always called with the --nobet option when using the GUI.
--So I thought if using the GUI, melodic could not include bet. Is it
right? And in fact, when I use melodic GUI, the melodic.log always show me --nobet, every time, whether or not I choose bet.
(2)
--After melodic analysis with command line function, I found in
melodic.log that: Calling BET: /usr/local/fsl/bin/bet /tmp/tcac.0
/tmp/tcac.0_brain -m -f 0.4 > /dev/null
Since -f 0.4 is not 0.3, so I thought that in melodic, bet instead of betfunc is used. Is it right?
hope your clarification.
Regards,
wei
Hi,
when you use the GUI instead of the command line then betfunc is
already used to find the mask which is then being passed to the
melodic binary
hope this helps
christian
On 24 May 2007, at 12:59, pengxu wei wrote:
> Dear
Christian,
>
> Thank you.
>
> It is introduced that betfunc uses a -f 0.3 for 4D fmri data while
> I found bet in Melodic uses a -f 0.4. Bet in melodic cut off the
> most top slice of my data but betfunc didn't. I think it is better
> for my data to use betfunc first then pass the mask made to melodic
> explicitly, as you said.
>
> Regards,
>
> wei
>
> Christian Beckmann <[log in to unmask]>写道：
> Hi
>
> melodic uses a different approach to robustifying bet for 4D data. In
> betfund, the inital mask is generated from the first image and then
> dilated by 1 voxel in x,y and z before masking all volumes by this
> new dilated mask. In melodic the bet outline is found by running bet
> on the mean image across time. I have not evaluated the differences
> explicitly but guess that they are small. Note that you can always
> pass a
mask to melodic explicitly by using the -m option
> cheers
> christian
>
>
>
> On 23 May 2007, at 15:49, pengxu wei wrote:
>
> > Dear list,
> >
> > I have read some message in the archive but no answer available.
> > betfunc is better than routine bet for 4D fmri data, so whether bet
> > in Melodic is betfunc(when using GUI or command line), or just
> > routine bet?
> >
> > Regards,
> >
> > wei
> >
> > 抢注雅虎免费邮箱3.5G容量，20M附件！
>
> ____
> Christian F. Beckmann
> University Research Lecturer
> Oxford University Centre for Functional MRI of the Brain (FMRIB)
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
> tel: +44 1865 222551 fax: +44 1865 222717
>
>
>
雅虎免费邮箱3.5G容量，20M附件！
____
Christian F. Beckmann
University Research Lecturer
Oxford University Centre for Functional MRI of the Brain (FMRIB)
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
[log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann
tel: +44 1865 222551 fax: +44 1865 222717
