Hi
if you want to concatenate the 4t dimension with avwmerge (or ++)
you'll need to use the -t option. The final results should always be
4D, not 5D. If melodic does not finish when using option1 what
exactly is the error message? Wrt both options note that when
transforming all images (or IC maps) to a common space you don't need
to upsample to 2mm resolution. If you have all the transformation
matrices computed then you can transform a 4D data set into standard
space while keeping it at e.g. 4x4x4mm resolution using flirt
flirt -in 4D -ref ${FSLDIR}/etc/standard/avg152 -out 4Dstd -
appyisoxfm 4 transformation.mat
hope this helps
Christian
On 30 May 2007, at 21:56, Peter Fried wrote:
> Hi,
>
> I am having some frustrations while trying to conduct a meta-
> analysis of
> resting-state FMRI data. Hopefully someone can help.
>
> So far, I have processed the raw data using pre-stats in FEAT and run
> MELODIC on each subject in their native space.
>
> Following the history of posts on this issue, I have tried both of the
> following using a test case of 4 subjects:
>
> 1) Transformed each subject's filtered_func_data (feat output) file to
> standard space; concatenated the data together across time using
> avwmerge++ -z; run melodic on the new 5D file.
>
> Problem: melodic finishes in < 5 sec w/ no results.
>
> 2) Transformed each subject's melodic_IC file (melodic output - 30
> components) to standard space; smoothed the data using a 5 mm Gaussian
> kernel (avwmaths++ -fmean -kernel gauss 5); concatenated the data
> together
> across time (avwmerge++ -z); run melodic on the new 5D file.
>
> Problem: melodic hangs in the command window while eating up most
> available CPU speed and RAM (after 30 minutes of 0 progress I
> killed the
> process).
>
> It certainly seems possible that method (2) may eventually work,
> but if it
> takes all available CPU and most RAM over an extended period of
> time for
> only 4 subjects, I'd hate to see what happens when I run it on 60+.
>
> I'm not sure what's going on with method (1) since I have no problem
> running melodic on an individual subject's filtered_func_data.
>
> Any suggestions on what I'm doing wrong or alternative methods to
> attempt
> would be much appreciated.
>
> Cheers,
>
> Peter Fried
> Center for Magnetic Resonance Research
> University of Minnesota
____
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
|