Hi.
On 30 May 2006, at 19:58, Katie Karlsgodt wrote:
> Hi,
> ok, thanks, I'll try out averaging the TBSS data within the ROI
> and see
> how doing stats on that goes.
> I still want to be sure I'm clear on my original process,
> though. So, to
> demean I would just do avwsplit on all_FA_skeletonised, merge each
> group
> into its own 4d file, do avwmaths -Tmean, split it again so that I can
> subtract the appropriate mean from each file, and then merge it all
> together
> into one big file? (or is there an easier way?).
Not quite, no. Use avwroi to split the 4D into two smaller 4D. Also -
Tmean will give you the mean 3D image which you should then subtract
from the 4D in avwmaths, before recombining the two halves.
Though actually - it's just occurred to me that there's an easier way
to demean the two group - create a 2EV group-mean modelling design
matrix and pass this into randomise with the -x flag - this then gets
regressed out of the data as the first step. Sorry for not thinking
of this last time!
> I think maybe I am a bit confused about some of the differences
> between
> randomise and Feat. If in addition to my existing EVs with demeaned
> behavioral data, I put in two more EVs that each code for a group
> (1's and
> 0's), would that also model the group mean FA (and make the manual
> demeaning
> unnecessary), or is randomise different with regards to this? I know
> covariates of non-interest have to be modeled in a separate design
> matrix,
> but am not sure whether that also means that this would not work?
Aha - yes, you're thinking along similar lines to what I just wrote
above - though it's better to include these "confound" group mean EVs
with the -x option rather than in the main design matrix when using
randomise, because in general there are issues of orthogonality in
permutation testing that are more complex than in FEAT-like simple
GLM. See Tom's paper for more details on the limitations of
permutation testing.
Cheers, Steve
> thanks,
> Katie
> ___________________________________
> Katie Karlsgodt
> Dept of Psychology/Cognitive Neuroscience
> University of California, Los Angeles
>
> [log in to unmask]
> phone: (310) 794-9673
> fax: (310) 794-9740
>
>
>
>> From: Steve Smith <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Date: Tue, 30 May 2006 07:48:21 +0100
>> To: <[log in to unmask]>
>> Subject: Re: [FSL] DTI ROI analysis
>>
>> Hi Katie,
>>
>> Sounds good. If you're using randomise (as opposed to FLAME) there's
>> no point setting the group membership IDs in the Glm GUI - randomise
>> doesn't use this information.
>>
>> If you already have a tract ROI defined, you might get more sensitive
>> results by averaging the TBSS-preprocessed data within the ROI and
>> then doing stats on the single summary number across subjects - but
>> what you're doing is fine too.
>>
>> It sounds like you are not modelling the group mean FA though! If you
>> just have 2 EVs, containing demeaned behavioural data, then you also
>> need to demean the data - i.e. demean each groupt separately before
>> re-concatenating to all subjects' 4D file and running randomise -
>> otherwise your model-fitting in randomise won't make sense...
>>
>> Cheers.
>>
>>
>> On 29 May 2006, at 20:13, Katie Karlsgodt wrote:
>>
>>> Hi,
>>> I'm trying to run an ROI based analysis in TBSS/randomise and
>>> would like
>>> to check whether what I'm doing is appropriate. I have a tract of
>>> interest,
>>> which I defined on the regular FA map and drew a mask of. I then
>>> masked out
>>> the portion of that tract that was included in the TBSS-skeleton
>>> using
>>> avwmaths. I ran randomise, using the skeleton masked tract as the
>>> mask in
>>> the -m option. I would like to see differences between groups in
>>> how FA of
>>> the tract relates to a behavioral measure. I created 2 groups in
>>> the group
>>> column, and entered 2 EV's, one with demeaned behavioral data for
>>> one group,
>>> and one with demeaned behavioral data for the other group. My
>>> contrasts then
>>> compare them (1 -1 and -1 1). I can't find anything on the list
>>> quite about
>>> this sort of thing, so just wanted to make sure this whole
>>> process is
>>> kosher? Thanks very much.
>>> Katie
>>> ___________________________________
>>> Katie Karlsgodt
>>> Dept of Psychology/Cognitive Neuroscience
>>> University of California, Los Angeles
>>>
>>> [log in to unmask]
>>> phone: (310) 794-9673
>>> fax: (310) 794-9740
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> ---
>> 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
>> ---------------------------------------------------------------------
>> ---
>> ---
>>
>>
------------------------------------------------------------------------
---
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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