Hi John
we do have some scripts around that will create webpages of snapshots, and in the upcoming release freeview will also support the syntax:
freeview -v vol.mgz:structure=17 ...
to automatically compute the slice that contains the most of label 17 (left hippocampus in this case). You can also specify the slice orientation and that it should take a snapshot and exit. The nmovie utility is then handy for zipping through a bunch of snapshots.
Note that putting together a pipeline for easy reviewing of large numbers of datasets is something we are going to be working on. Also, you might check with JB Poline (ccd), as I know it's something he has thought about seriously.
cheers Bruce
On Thu, 14 Apr 2011, McLean John (NHS Greater Glasgow & Clyde) wrote:
I'd like to create some summary images (.tiff, .png ) so that I can quickly inspect subcortical structure segmentation quality on a large number of subjects.
I know I can open tkmedit and extract a series of tiff images, I've also been playing with Slicer3 but again I have to load the data for each subject.
I'd also like to hone in on particular structures, for example, to extract images only showing the hippocampus (whole segmentation or outline) on the T1 3D backdrop, does anything exist in Freesurfer to do this from the command line?
Essentially I'm looking for something similar to the first_roi_slicerdir command in FSL as I found this a really quick way of visually checking segmented data.
Any advice around this would be a great help,
Thanks John
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