[MINC-users] Blurring a 4D minc volume?

[Michael Ferreira]

Hi Jim,

Have you tried fmr_preprocess?  It's not part of the standard MINC 
install, but it is available on most BIC machines.  We normally use it 
to motion-correct and blur fMRI data.  But you can turn off the 
alignment part with the -noalign option, and specify the amount of 
blurring in millimeters with the -fwhm option:

/usr/local/mni/bin/fmr_preprocess -noalign -fwhm 6 input.mnc

This script should preserve the time info.  Nonetheless, you should 
verify the output.

Regards,

mike



EJ Nikelski wrote:
> Hi All,
> 
>    I seem to have hit a wall, and need some suggestions.  I have a 4D
> volume (time * z * y * x) which I need to blur. No problem, I think.
> So, I do the following:
> 
> (1) mincreshape to split the 4D volume into a series of 3D volumes
> (2) mincblur each separately
> (3) mincconcat to slap it all together again
> 
> Here's the problem: mincreshape actually produces a 4D volume with
> "time" the slowest varying dimension and equal to 1.  This is
> precisely what I want, since this preserves my time data (eg, time
> start, time-width).  This is important, since my times are *not*
> fixed.  mincblur then comes along and, more or less, corrupts the
> volume in that the time dimension is still in the header -- but it's
> now as the fastest varying dimension, and all of its variable info has
> been removed.  At this point, the mincconcat stage is pointless, in
> that I have now lost my time info.
> 
> What's the best way to get around this, while retaining my "irregular"
> time information? Suggestions? Ideas?
> 
> 
> -Jim
>