Right on. So you mean--you should always perform motion correction, but whether or not to regress it out at first level analyses is what should be evaluated?
I always check the quality of my data when it is completely preprocessed anyway-creating plots of motion and data across time series. I can just probably add a plot of stimulus timings to that script.
Christine

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
Sent: Wednesday, January 04, 2012 5:31 PM
To: [log in to unmask]
Subject: Re: [FSL] confoundevs.txt

Dear Christine,

You can look at the motion correction plots and see if jumps tend to
align with stimuli, or you can numerically calculate the correlations.
Depending on your experiments it may not be too bad, but we have
definitely seen several (e.g. pain experiments) where motion and
stimulus were tightly correlated and so this kind of simplistic correction
for motion artefact is too strong and removes all the true activation.
Therefore I would never recommend that you include it automatically
without also looking at the result without this correction. Note that this
is all about the inclusion of motion parameters in the GLM as confounds.
It is *not* about the *motion correction* step (with mcflirt) which should
*always* be run.

If you have strongly correlated motion then there are other methods for
dealing with the artefact, such as fsl_motion_outliers and ICA-based
cleanup.

All the best,
Mark


On 4 Jan 2012, at 22:26, Christine Zakrzewski wrote:

> Dear Mark.
> How would you know if the motion and stimulus presentation were correlated?
> So--do you think we should make motion correction an automatic step in preprocessing pipeline, or do we have to check something first?
> Christine
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
> Sent: Wednesday, January 04, 2012 4:52 PM
> To: [log in to unmask]
> Subject: Re: [FSL] confoundevs.txt
>
> Dear Jiansong,
>
> The file contains whatever you, as the user, has decided to include.
> You can have motion parameters, or not.
> You can have spikes, as detected by fsl_motion_outliers, or otherwise, or not.
> FEAT itself doesn't believe anything - it is the user that must decide.
> There is also no general consensus on what is good to include or not, as it
> somewhat depends on the nature of the motion. With highly stimulus correlated
> motion, including the motion parameters can cause the activation to disappear.
> So I can't help you out on this one with a simple rule of thumb I'm afraid.
>
> All the best,
> Mark
>
>
>
> On 4 Jan 2012, at 18:56, Jiansong Xu wrote:
>
>> Hi, Mark:
>>
>> Does this file contain motion parameters and other data (e.g., spikes) FEAT believe they should be controlled during stats?
>>
>> Best Regards
>>
>> Jiansong
>>
>> The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to [log in to unmask] and destroy this message. Please be aware that email communication can be intercepted in transmission or misdirected. Your use of email to communicate protected health information to us indicates that you acknowledge and accept the possible risks associated with such communication. Please consider communicating any sensitive information by telephone, fax or mail. If you do not wish to have your information sent by email, please contact the sender immediately.
>> ===============
>> Jiansong Xu, M.D., Ph.D.
>> Assistant Professor
>> Dept. of Psychiatry
>> Yale Medical School
>> 1 Church St., Room 729
>> New Haven, CT 06519
>> Tel: 203-785-5306
>> Fax: 203-737-3591
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Jan 3, 2012, at 10:09 AM, Mark Jenkinson wrote:
>>
>>> Dear Jiansong,
>>>
>>> It is just a text file containing the values of the EVs at each time point
>>> arranged as a N by M matrix where N is the number of timepoints (rows)
>>> and M is the number of EVs (columns). It is simply appended (columnwise)
>>> to the design matrix before running the stats.
>>>
>>> Hope this helps.
>>> All the best,
>>> Mark
>>>
>>>
>>> On 3 Jan 2012, at 14:31, Jiansong Xu wrote:
>>>
>>>> Hi, Mark:
>>>>
>>>> Thanks. Now, let me ask the question a little bit differently.
>>>>
>>>> What is inside the confoundevs.txt, and how to use it?
>>>>
>>>> Best Regards
>>>>
>>>> Jiansong
>>>>
>>>> The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to [log in to unmask] and destroy this message. Please be aware that email communication can be intercepted in transmission or misdirected. Your use of email to communicate protected health information to us indicates that you acknowledge and accept the possible risks associated with such communication. Please consider communicating any sensitive information by telephone, fax or mail. If you do not wish to have your information sent by email, please contact the sender immediately.
>>>> ===============
>>>> Jiansong Xu, M.D., Ph.D.
>>>> Assistant Professor
>>>> Dept. of Psychiatry
>>>> Yale Medical School
>>>> 1 Church St., Room 729
>>>> New Haven, CT 06519
>>>> Tel: 203-785-5306
>>>> Fax: 203-737-3591
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Jan 3, 2012, at 9:09 AM, Mark Jenkinson wrote:
>>>>
>>>>> Dear Jiansong,
>>>>>
>>>>> I think this is more a question for the SPM list than the FSL list.
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 3 Jan 2012, at 13:55, Jiansong Xu wrote:
>>>>>
>>>>>> Dear All:
>>>>>>
>>>>>> I have a funny question.
>>>>>>
>>>>>> I used FEAT for preprocessing and would like to use SPM for stats. My question is:
>>>>>>
>>>>>> Can I input confoundevs.txt generated by FEAT into SPM5 single subject analysis to control motion, spikes, and other confounders?
>>>>>>
>>>>>> Best Regards
>>>>>>
>>>>>> Jiansong
>>>>>>
>>>>>> The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately with a copy to [log in to unmask] and destroy this message. Please be aware that email communication can be intercepted in transmission or misdirected. Your use of email to communicate protected health information to us indicates that you acknowledge and accept the possible risks associated with such communication. Please consider communicating any sensitive information by telephone, fax or mail. If you do not wish to have your information sent by email, please contact the sender immediately.
>>>>>> ===============
>>>>>> Jiansong Xu, M.D., Ph.D.
>>>>>> Assistant Professor
>>>>>> Dept. of Psychiatry
>>>>>> Yale Medical School
>>>>>> 1 Church St., Room 729
>>>>>> New Haven, CT 06519
>>>>>> Tel: 203-785-5306
>>>>>> Fax: 203-737-3591
>>>>>>
>>>>
>>
>
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