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

[EJ Nikelski]

Hi List,

   OK, I've got a work-around, which I shall document for google
posterity (and for whomever else runs into this).  The solution looks
like this (a la Wittgenstein):

1.0 Understand that ripping a 4D volume apart loses you stuff
1.1 Prior to dismembering your 4D volume, have your script save the
important stuff (etc, time, time-width,etc)
1.2 Dismember (mincreshape, why not?)
2.0 blur
3.0 recombine with mincconcat, paying special attention to the
-coordlist and -widthlist arguments.

   That's all.  Pretty simple, if you go to sleep thinking of
mincconcat switches ... and if you realize that -coordlist is really
all about frame start times, when dealing with time as your 4th
dimension.

Cheers,

-Jim




On Thu, Feb 19, 2009 at 6:36 PM, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
> 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
>>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> --
> =================================
> 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
>



-- 
=================================
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