It might be interesting to compare DVARS pre- and post-FIX. But I don’t
see that as very meaningful for FD. i.e., if you supplied motion
realigned data to FIX, then using ‘fsl_motion_outliers’ to generate an
“FD” estimate post-FIX is simply going to return an estimate of whether
there is any “residual motion” present in the data after you’ve already
done motion realignment.
You can certainly average the values across time points for a given
subject, if you choose to use that as a summary measure.
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: [log in to unmask]
On 9/13/16, 9:27 AM, "FSL - FMRIB's Software Library on behalf of
Christiane Jockwitz" <[log in to unmask] on behalf of
[log in to unmask]> wrote:
Dear Michael,
I used the motion corrected data to run FIX. I’m interested in how the
motion parameters change after running FIX.
so, then I would use my raw EPI data (before running mcflirt) as input and
calculate the different values (FD, DVARS and RMS).
e.g. fsl_motion_outliers –i raw_data_EPI.nii.gz –o FD –fd –s fd.txt
and as a second step I would use the filtered_func_data_clean as input
image and then run fsl_motion_outliers for the different values
(FD,DVARS,RMS).
e.g. fsl_motion_outliers –i filtered_func_data_clean.nii.gz–o FD –fd –s
fd.txt
Is that correct?
And as a second question, I would like to have only one value for FD,
DVARS and RMS for each subject. Would it be then correct to calculate the
mean of all values in my txtfile?
Thank you very much in advance.
Best
Christiane
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