Hi,
Note that the -m option in FIX simply regresses out the variance related
to the motion parameter estimates. FIX itself doesn’t actually motion
correct your data. Usually ones supplies motion corrected data (e.g,.
MCFLIRT) as the input to FIX.
cheers,
-MH
--
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 9/11/16, 10:18 AM, "FSL - FMRIB's Software Library on behalf of
Christiane Jockwitz" <[log in to unmask] on behalf of
[log in to unmask]> wrote:
Dear FSL experts,
I would like to calculate motion estimates (DVARS, FD, RMS) for my already
preprocessed subjects. I would like to compare the motion parameters
before doing FIX (including the motion correction within FIX; -m) and
afterwards.
1.To calculate the motion parameters BEFORE FIX I used the raw EPI data
as input:
Fsl_motion_outliers –i raw_data_EPI.nii.gz –o FD –fd –s fd.txt
I averaged the motion parameters by calculating the mean of all
parameters in the textfile
2.To calculate the motion parameters AFTER FIX I used the
filtered_func_data_clean:
Fsl_motion_outliers –i filtered_func_data_clean.nii.gz–o FD –fd –s
fd.txt
I averaged the motion parameters by calculating the mean of all
parameters in the textfile
Is that the right way to calculate and compare motion parameters BEFORE
and AFTER FIX?
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