I'm trying to run a group analysis with flameo with NIfTI input files
generated from another FMRI data analysis package. The following are
a beginner's questions about flameo:
1. Although I provided a mask for running the analysis, in the end
flameo generated a new mask in the result directory that is smaller
than my original mask. I also noticed the following message on the
terminal:
"WARNING: The passed in varcope file, myInput_var.nii.gz, contains
voxels inside the mask with zero (or negative) values. These voxels
will be excluded from the analysis."
Does it mean that wherever there is ZERO variance for one or more
subjects at a voxel, that voxel would be masked out in the analysis?
2. I tried to turn on the button for "Use automatic outlier de-
weighting" on FSL GUI interface, but it seems the *.mat, *.con, and
*.grp saved from the GUI don't really change compared to the ones
when the button is turned off. So if I want to infer outliers, is the
option --io not the button on the GUI, the correct way to go with
flameo?
3. I know I could use the z-score in the output for thresholding, but
if I want to play with the t-stat, how can I threshold the t-stat
combined the degrees of freedom file with FSLview especially each
voxel has its own DOF?
Thanks in advance,
Gang
|