I would use FSL's ICA+FIX to deal with residual movement artifacts.
Peace,
Matt.
On 3/1/16, 10:40 AM, "FSL - FMRIB's Software Library on behalf of Colin
Hawco" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>With regards to the motion question I think you should almost certainly
>include these regressors in all subjects.
>
>I offer a practical reason for doing so: if you do not, a reviewer likely
>will shoot you down for it. They will assert, not incorrectly, that
>different subjects have been treated differently, and this may have
>unpredictable effects on your results.
>
>If you are moving to a second level analysis, the loss of degrees of
>freedom
>in the first level shouldn't matter much.
>
>However, as a caveat, motion regressors do a poor job of controlling for
>motion. The motion parameters are an estimate of overall movement within a
>TR< and would be valid if people made sudden specific motions only in
>between TRs. This isn't the case, and the motion parameters often poorly
>estimate actual motion.
>
>And if you look at voxel time courses, motion artifacts often peak after
>the
>TR in which the spike appears in the parameters.
>
>There are scrubbing options you can choose. You can censor and/or
>reinterpolate TRs with motion, plus an additional TR or 2. AFNI's despike
>option can also help, as it removes outlier from the voxel time series
>(independent from the motion parameters). Also, there are approaches such
>as
>Daimien Faire's and Ted Satterthwaite's approaches which include more
>extensive motion paramters.
>
>Good luck,
>
>Colin Hawco, PhD
>Neuranalysis Consulting
>Neuroimaging analysis and consultation
>www.neuranalysis.com
>[log in to unmask]
>
>
>
>-----Original Message-----
>From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>Of Matthew Webster
>Sent: March-01-16 11:00 AM
>To: [log in to unmask]
>Subject: Re: [FSL] Motion Outliers + Physiological Noise Model
>
>Hi Ella,
> Thank you for your upload, unfortunately it isn't clear what
>is failing from the logs. Can you tar and upload the full FEAT directory
>to:
>
>https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
>
>Kind Regards
>Matthew
>
>> Hi all,
>>
>> I'm running a set of first level Feat analyses on task-related BOLD
>activation in 20 participants, in which some of the participants have
>moved
>more than a voxel-worth. I have therefore included the motion outliers
>confound file in the analyses.
>>
>> My first question is: should motion outliers be run all participants in
>the study or is it okay to only include this confound file for only those
>who have moved excessively?
>>
>> As this confound file reduces the dof in the GLM, I am keen not to do
>>this
>unnecessarily, but my instinct was to be consistent across all
>participants.
>Can you advise?
>>
>> I also ask as we also have physiological noise modelling for this
>>dataset.
>This also generates a confound file. We have both motion outliers and Pnm
>confounds for 18/20 participants, but the first level analyses have failed
>for 14/18 of them. It runs the Stats section, then an error occurs at
>Post
>Stats so none are computed. Here is the error message (taken from the
>Stats
>section into the Post-Stats section in case helpful):
>> Log directory is: stats
>> paradigm.getDesignMatrix().Nrows()=1598
>> paradigm.getDesignMatrix().Ncols()=131
>> sizeTS=1598
>> numTS=117655
>> Calculating residuals...
>>
>> Post-stats
>>
>> child process exited abnormally
>> while executing
>> "if { [ catch {
>>
>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>> switch -- [ lindex $argv $argindex ] {
>>
>> -I {
>> incr arginde..."
>> (file "/usr/local/fsl/bin/feat" line 309) Error encountered while
>> running in main feat script, halting.
>> child process exited abnormally
>>
>> My second question is: does anyone know a reason why this error is
>occurring or how I can investigate where in the script the error is
>encountered? I assumed it was just the impact of including both sets of
>confounds, but as 3 have so far run without issue, this can't be the
>reason.
>>
>> I would be extremely grateful for your help, With best wishes Ella
>> Hinton
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