Thanks a lot! Quick follow up question:
Is the best command for
> "Next threshold each into a binary mask."
fslmaths example_mask -thr .5 -bin example_mask ?
(or would a different threshold value be recommended for the current purpose?)
Thanks again,
Regina
Thanks!On Fri, 17 Apr 2009 13:24:06 +0100, David Flitney
<[log in to unmask]> wrote:
>Hi,
>
>On 17 Apr 2009, at 12:53, Regina Carla Lapate wrote:
>
>> 2)Based on pre-defined ROI masks, such as the ones found here:
>> $FSLDIR/data/atlases/HarvardOxford-Cortical.xml
>> run some type of "concatenate" command that would create a PFC mask
>> containing all the cortical PFC ROIs.
>
>Assuming they have the coverage you need then this is pretty easy to
>do: using the probabilistic atlases extract the individual probability
>volumes (this can be done using the fslview atlas tool "Structures..."
>dialog to "+" them into the overlay list then "Save as..." to write
>them into separate files). Next threshold each into a binary mask.
>Finally use fslmaths to "OR" them together: "fslmaths A -max B -max
>C.... -bin PFC_std_mask" should do the trick.
>
>--
>Dave Flitney, IT Manager
>Oxford Centre for Functional MRI of the Brain
>E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
>URL: http://www.fmrib.ox.ac.uk/~flitney
>
>
>
>
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