Hi Greg,
I ran some more subjects and I checked the resulting image for one of them.
This subject had 0.6mm total displacement over the 900 volumes, no spikes, all
smooth constant displacement through the timeseries. I used mcflirt to do that
registration. In this image
What is the resolution of this fMRI data? I seem to recall someone else
had trouble with the motion correction pipeline on lower resolution data.
It may be that we need to allow an option for mcflirt in the pipelines if
the default method doesn¹t work for someone.
Peace,
Matt.
On 10/28/14,
Hi Tim,
Thank you for the help with the workbench and the code. Yes, it is a mac osx.
Sorry for the mix up.
Also, I can get the first two commands to work for MEAN and STDEV, but the
last command gives me an error message:
wb_command -volume-math '((x - mean) / stdev)' normalized.nii.gz
Hi Michael,
The animated gif has the raw timeseries
(SubjID/unprocessed/3T/resting/analysis_3T_resting.nii.gz) on top and the end
result of the HCP processing on the bottom
(SubjID/MNINonLinear/Results/resting/resting.nii.gz). Some of the big motions
are from volumes 450-600. The voxel size of
That is the error I would expect if you removed the -repeat after the -var
option for mean (yes, it needs 2 -repeat options, they each associate with
one -var option) - could you paste the command you actually ran?
Tim
On Tue, Oct 28, 2014 at 11:30 AM, Nomi, Jason jxn...@miami.edu wrote:
Hi
