HI - the extra voxels on the outer edge are just due to the smoothing
extending nonzero voxels outwards. I would take a mask from the
unsmoothed dataset and apply it to the outputs of the other ip calls.
Cheers, Steve.
On 18 May 2006, at 19:34, Martin M. Monti wrote:
> Hi,
>
> I'm processing some functional data - i.e. filtered_func_data - by
> smoothing it with IP
>
> Here's the relvant part of my code:
>
> echo "Smoothing 6mm"
> ip filtered_func_data_2Anat_0mm.nii.gz filtered_func_data_2Anat_6mm
> 10 -s 2.54777070064 -m mask -I 10000
> echo "Smoothing 9mm"
> ip filtered_func_data_2Anat_0mm.nii.gz filtered_func_data_2Anat_9mm
> 10 -s 3.82165605096 -m mask -I 10000
> echo "Smoothing 12mm"
> ip filtered_func_data_2Anat_0mm.nii.gz
> filtered_func_data_2Anat_12mm 10 -s 5.09554140127 -m mask -I 10000
>
> [with filtered_func_data_2Anat_0mm being the filtered_func_data
> from a "pre-stats ONLY" run of FEAT with no smoothing, aligned to
> the subject's anatomical via flirt.]
>
> Now, each smoothing yields a slightly different sized brain (I
> assume padding?). As a result, an ROI created on the *_0mm brain
> is in a different relative position to the side of the brain when
> overlayed on a 12mm smoothed functional than it is in the _0mm
> brain. For example one of my ROIs is exactly on the anterior Left
> border of the 0mm functional, whereas if I overlay it on the 12mm
> smoothed it's no longer on the border.
>
> My question is, are those voxels between the mask and the border of
> the smoothed brain meaningful voxels?
>
> Cause I'm a bit puzzled now on whether I should smooth the masks
> too, to get the mask to the same 'relative' size of the smoothed
> brain, or if I can keep on using my initial mask (I'm using it to
> pull out timecourses with avwmeants) since the extra voxels are non-
> meaningful ones and the position of my voxels of interest (those in
> the non-smoothed mask) didn't change (in terms of voxel 3D position)?
>
> I apologize if this isn't clear, let me know and I'll give it
> another shot!
>
> cheers
>
> Martin
>
> --------------------------
> "Upward, not Northward!" [Edwin Abbott - FlatLand]
>
> I became insane, with long intervals of horrible sanity. [E.A. Poe]
>
> Would you tell me, please, which way I ought to go from here?
> ''That depends a good deal on where you want to get to.'' Said the
> Cat. I don't much care where -- Said Alice. Then it doesn't matter
> which way you go, said the Cat. [Lewis Carroll]
>
> Che si trattasse di una gara? ..Un colpo il mondo e un colpo tu, a
> chi stupiva un po' di piu'.. [Per Un Vecchio Bambino - Roberto
> Vecchioni]
>
> --------------------------------------------
> Martin M. Monti
> Princeton University
> Department of Psychology
> Green Hall 3-S-8
> (609) 258-5679
> www.webmartin.net
> --------------------------------------------
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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