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

[EJ Nikelski]

Hi Mike (and minc-users List),

   Thanks for the suggestion, but as luck would have it, Yup -- I've
already tried fmr_preprocess.  It seems to preserve the time dimension
info well, however, it loses the time-width variable.  The time-width
variable contains the irregular frame durations (I'm working with
multi-frame PET volumes), and is something that I need to preserve.

   Now, I've heard that there may be multiple versions of
fmr_preprocess kicking around, so this may simply be a short-coming of
the version that I'm using.  If you were to point me to the best and
coolest version, I would certainly be prepared to give that a shot as
well.

Thanks,

-Jim


On Thu, Feb 19, 2009 at 5:08 PM, Michael Ferreira
<mferre at bic.mni.mcgill.ca> wrote:
> 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
>>
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-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University
Tel: (514) 340-8222 x 2298
Fax: (514) 340-8295