Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say "extract specific regions of functional data from a flat " do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths -mas option in
freesurfer.
I have several manually defined labels in .label form that I want to use to
extract specific regions of functional data from a flat patch. Ordinarily in
fsl I would just use
fslmaths -invol {functional_data} -mas {bin_label} -outvol
{masked_functional_data}
but I'm a little confused about an equivalent for this in free surfer as I
don't want to perform any further stats on these ROI yet, extract them from
any surrounding data and overlay onto the flattened surface.
I have tried using
mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
{anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
{func_V2_mask_out}
but when overlaying the output file there are no data points visible.
Any help would be great as several other functions that I have tried seem to
be obsolete,
Thanks!
Sarah
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