Hi
That's right, the GUI does call betfunc and let's the command-line
version know that no betting is required by setting the -nobet
option. Other than switching bet off inside melodic (either by
passing a mask in explicitly via -m or using --nobet) there is no way
to change the behaviour, i.e. you can't pass in command line options.
You could change the setting nside the code and compile for yourself,
though.
cheers
christian
On 25 May 2007, at 14:29, pengxu wei wrote:
> Dear Christian,
>
> 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.
>
> Regards,
>
> wei
>
> pengxu wei <[log in to unmask]> дµÀ£º
> Dear Christian,
>
> Thank you. but some further doubts induced from your reply...
>
> (1)
>
> Christian Beckmann <[log in to unmask]> дµÀ£º
> 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
> but from http://www.jiscmail.ac.uk/cgi-bin/webadmin?
> A2=ind03&L=FSL&P=R12990&D=0&I=-3&m=418
> : ...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)
>
> from http://www.fmrib.ox.ac.uk/fsl/bet/index.html:
> betfunc COMMAND-LINE SCRIPT...the -f threshold is reduced to 0.3...
>
> --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
>
> Christian Beckmann <[log in to unmask]> дµÀ£º
> 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 дµÀ£º
> > 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
> > >
> > > ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä3.5GÈÝÁ¿£¬20M¸½¼þ£¡
> >
> > ____
> > 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
> >
> >
> > ÑÅ»¢Ãâ·ÑÓÊÏä3.5GÈÝÁ¿£¬20M¸½¼þ£¡
>
> ____
> 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
>
> ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä3.5GÈÝÁ¿£¬20M¸½¼þ£¡
>
>
> ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä3.5GÈÝÁ¿£¬20M¸½¼þ£¡
____
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
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