External Email - Use Caution
Hi Bruce,
Thanks for that reminder about the flat maps as patches. I typically use the
flat maps after conversion to gifti, so they are then their own full surfaces.
With the center away from (0,0,0), the patch does indeed show up, but it's out
of the usual view, so I have to zoom out to see it. I've recentered the surface
to be around 0,0,0 to make this a little easier. It might be helping with the
flattening too because I'm getting close to a good result. Sometimes the
randomness of the flattening process fails, but a retry can work, occasionally
requiring a few tries. The terminal output includes the random seed used, so I
can use that if I were to rerun the mris_flatten.
I still have an important issue in that there is an artifact of either one or
two round swirls of misplaced nodes. These can be inside the contiguous flat
map or even outside the flattened map as a separate circle, away from the rest
of the flat surface. For the interior swirls, it's easier to visualize that
with some annotation mapped from the original surface to the flat map. I did
that visualization with suma because I know that better, but I can see the same
swirls in the surface mesh using freeview. These are the steps I've taken so
far. Do you have any recommendations?
Thanks,
Daniel
mkdir surf
# put initial data in the directory
cp somedir/isosurf.gii surf/
cd surf
mris_convert isosurf.gii lh.smoothwm.3d
mv lh.smoothwm.3d lh.smoothwm
# make cuts on surface in GUI
freeview
# load surface. make series of cuts using GUI (mark points, Scissors - open
path)
# save as patch lh.mycut.flat.3d
# flatten cut data
# increasing the distances to 10 10 and dilation to 8 moves the swirl outside
mris_flatten -distances 5 5 -dilate 4 lh.mycut.3d lh.mycut.flat.3d
# convert flat map to gifti surface
mris_convert -p lh.mycut.flat.3d lh.smoothwm.flat.gii
# make spec file for suma
quickspec -spec my_surfaces.spec -tsnad gii surfacename lh.smoothwm.gii Y SAME \
-tsnad gii flat lh.smoothwm.flat.gii N lh.smoothwm.gii
[cid:[email protected]]
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
