Can you try re-run that freeview command again? I remember I saw similar
problem once, but somehow I could not reproduce it when I re-run the
same command. If you can positively reproduce it, would it be possible
to send us all the files that are used in the command?
Best,
Ruopeng
On 6/26/12 3:41 AM, Chao Suo wrote:
Hi all,
I am new with freesurfer, and I found a problem when processing some
data following the instruction online.
When I checked the surfaces of these two timepoint together using
freeview (follow the instruction online), it showed this abnormal
spike on the white mater surface of my time point two scan. (fig 1,
left, clear version: https://dl.dropbox.com/u/4825915/fig1.png)
freeview -v SMART001aT1.long.SMART001T1/mri/norm.mgz \
SMART001bT1.long.SMART001T1/mri/norm.mgz \
-f SMART001aT1.long.SMART001T1/surf/lh.pial:edgecolor=red \
SMART001aT1.long.SMART001T1/surf/lh.white:edgecolor=blue \
SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \
SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \
However, it was wired that I couldn't see this spike when I opened
them in tkmedit. (fig1, right, https://dl.dropbox.com/u/4825915/fig1.png)
tkmedit SMART001bT1.long.SMART001T1 brainmask.mgz -aux wm.mgz --surfs
Further, if I inspected only the two surfaces of my time two data,
there is no such spike at the same point. (fig2, clear version:
https://dl.dropbox.com/u/4825915/fig2.png)
freeview -v SMART001bT1.long.SMART001T1/mri/norm.mgz \
-f SMART001bT1.long.SMART001T1/surf/lh.pial:edgecolor=255,128,128 \
SMART001bT1.long.SMART001T1/surf/lh.white:edgecolor=lightblue \
So I am not sure whether these spikes are bugs when using freeview, or
actually some registration error that need me to edit. Can some help
me to confirm it? Or, did anyone come across this problem before?
Thanks
Chao Suo
--------------------------------------------
PhD Candidate, School of Psychiatry, UNSW, Australia
Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY
Room 401, Level 4, M02K | 100 Mallett St Camperdown | NSW | 2050
T +61 2 9351 0728 | F +61 2 9351 0551 |
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
