Steve,
got it, thanks!
martin
----- Original Message -----
From: "Steve Smith" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Friday, May 19, 2006 8:15 AM
Subject: Re: [FSL] IP and border expansion:meaningful voxels?
> 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
>> --------------------------------------------
>>
>
>
> ------------------------------------------------------------------------
> ---
> 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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