To follow-up on this: For some reason, the ICA's no longer converge (the log file below has "Registration to standard image" set to 1, but it does not work even if it is set to 0).  I've attached the design file and log file. I'd be grateful for any directions towards resolving the issue. 

Thanks again,

AB

On Mon, Nov 16, 2015 at 9:11 AM, AR Bala <[log in to unmask]> wrote:

Thank you very much Paul! That is exactly what happened - I'd used the 'mean functional' as the background image.

On Mon, Nov 16, 2015 at 5:37 AM, paul mccarthy <[log in to unmask]> wrote:

Hi AB,

Did you select 'Mean functional' as the background image on the Melodic GUI post-stats tab? If so, the all-white background is probably due to the fact that all of the individual voxels within a residual image are de-meaned.

You can either choose a different background image (structural or standard). Or, if you really want the functional data as your background, you could add the mean of the original data to your res4d image before running Melodic. This will make your data 'look' more like a functinoal image, but won't change the melodic results.

Cheers,

Paul

On 15 November 2015 at 16:59, Ar B <[log in to unmask]> wrote:

Hello all,

I've concatenated 2 resting state res4d scans, and tried to run MELODIC on the concatenated registered res4d data (because I had already done registration, I set all registrations for the melodic.fsf design file to 0, also taking note of the comments in this thread: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1511&L=fsl&F=&S=&X=405BDF168924D4B110&Y=arb.edqueries%40gmail.com&P=200122

I am able to generate components without errors, but on viewing the ICs, I see the images as completely white (sample component slices screenshot attached). I do see areas of activation that are interpretable, but why is it that the ventricles and other "dark" areas that should be present in the image aren't seen?

I appreciate all your help, and apologize if this should be obvious!

Best,
AB