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Stephen,

Thank you for your advice.

I figured that I would try and regress out the confounders and perform individual ICA exploration using FEAT. This step would be performed on data that have been pre-processed through WM/CSF regression (and obviously the motion correction performed in fsl_motion_outliers).

that's OK as an exploratory approach - however, normally if you are going to apply both ICA cleanup and confound-regressor cleanup, we would recommend running the ICA first.

Would you also suggest using FIX after doing this, or is that overkill?

same answer - ICA+FIX is logically the same as ICA cleanup with manual artefact component identification

Also, as for training the FIX classifier: since I have AD and healthy control subjects, should I use equal numbers of both groups in the 10 or so training subjects?

Yes I would think so.

Cheers.

Thanks again

On Wed, Jul 23, 2014 at 4:43 AM, Stephen Smith <[log in to unmask]> wrote:

Hi

On 22 Jul 2014, at 17:03, Paul Beach <[log in to unmask]> wrote:

FSL experts and users,

I'm working toward an ICA analysis on healthy controls and AD patients for the first time and thus I am very interested in making sure I appropriately deal with motion confounds.

I've been looking through past message board correspondence on this topic and I can't seem to find anything too conclusive wrt just when/where to include the fsl_motion_outliers output as a confound EV (specifically using the Power (2012) methodology).

It seems like the most recent discussion about this topic suggested doing so at the single subject level, PRIOR to doing any group ICA/dual-regression steps (i.e. doing a single-subject melodic run and including the output in the post-stats model/contrast). Is this correct?

Nearly - though I would recommend that if your main analysis is group-ICA followed by dual regression, then you should do within-subject cleanup - either using FIX, or regressing out confounds like motion-outliers, etc.

Some of the messages also discuss interest in developing a melodic-based classifier to automatically pick out/remove motion-based components. This is yet to be incorporated in FSL, correct?

This is FIX, which is released as an FSL "plugin" now.

Cheers.

What are other folks doing to address this issue?

Thanks
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU Cognitive and Geriatric Neurology Team (CoGeNT)

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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
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[log in to unmask] http://www.fmrib.ox.ac.uk/~steve

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Stop the cultural destruction of Tibet

--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- MSU Cognitive and Geriatric Neurology Team (CoGeNT)