Hi Paul,
Yes, the workflow looks good to me!
Kind Regards
Matthew
> Hi Matthew,
>
> So you're saying that the steps should be:
>
> 1. FEAT+ICA
> 2. Remove bad components (either manually+fsl_regfil...or with FIX?)
> 3. use FEAT stats only on the output from #2.
>
> Does that sound correct?
>
>
> On Thu, Jul 24, 2014 at 11:40 AM, Matthew Webster <[log in to unmask]> wrote:
> Hi Paul,
> If you have run Melodic ICA as part of a full FEAT analysis then no actual denoising will have occurred - to do this you need to run in Preprocessing only mode to generate the ICA report and then use fsl_regfilt to denoise ( see the FEAT user guide for details ). The additional confound EVs file will then be applied when Statistics only mode is run on the denoised data.
>
> Kind Regards
> Matthew
>> Ok. Thank you.
>>
>> It looks as though, according the the report.html logs that this is what FEAT does is you select both ICA exploration and additional confound EVs (i.e. the .txt output from fsl_motion_outliers).
>>
>> However, I'm still not clear about one part of my question.
>>
>> After doing the exploratory ICA followed by confound regressor cleanup would it then also be a good idea to further remove components (say, with FIX), or is that too much?
>>
>> I'm sorry to pester with this questioning, but I really want to make sure that I'm not plagued with motion confounds since these are data that include severe Alzheimer's patients.
>>
>>
>> Cheers
>>
>>
>> On Thu, Jul 24, 2014 at 5:24 AM, Stephen Smith <[log in to unmask]> wrote:
>> HiOn 23 Jul 2014, at 13:28, Paul Beach <[log in to unmask]> wrote:
>>
>>> 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)
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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
>>> ---------------------------------------------------------------------------
>>>
>>> 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)
>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>>
>> 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)
>
>
>
>
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - MSU Cognitive and Geriatric Neurology Team (CoGeNT)
