Hi,
I completely agree with Joe - concatenating the data is probably not
what you want since it will result in suboptimal motion-correction. The
reason is that (for 'typical' fmri experiments) the amount of motion
within one run is considerably smaller than between runs. When data is
concatenated mcflirt will register all the low-res fmri volumes to one
reference image (by default the middle one) which for all volumes from
the different runs other than the one that the ref. image belongs to
will make motion-correction less accurate.
If you really want to concatenate the data you'll probably have to do
some clever shell scripting. Usin avwroi instead of avwsplit will make
this a bit easier for you though...
cheers,
Christian
Joe Devlin wrote:
> Hi Russ,
>
>> hi all - I'm trying to motion-correct fMRI data collected over multiple
>> runs, and it's not clear how to do this with mcflirt at the command
>> line. Obviously I could do this using some combination of avwmerge and
>> avwsplit but that seems rather awkward, particularly because I would
>> have to reconstruct the numbering within the individual runs after
>> avwsplitting the merged motion corrected image. Any suggestions would
>> be greatly appreciated.
>
>
> I know this isn't really an answer but I'm wondering why you want to motion
> correct more than one run at a time? I typically motion-correct the runs
> individually, analyse them individually at the first level, and enter them
> into the second level as repeated measures now that Feat5 offers that
> option. I've found it works pretty well.
>
> Cheers,
> Joe
>
> Joseph Devlin, Ph. D.
> FMRIB, Dept. of Clinical Neurology
> University of Oxford
> John Radcliffe Hospital
> Headley Way, Headington
> Oxford OX3 9DU, U.K.
> Phone: +44 (0)1865 222 738
> Fax: +44 (0)1865 222 717
> Email: [log in to unmask]
>
>
--
Christian F. Beckmann
Address: Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7811 189123
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