Hi Roueng,

Thanks for your suggestion. Though I might reproduce it yesterday (can't remember), freeview works well today. I can't find any spikes like yesterday. (screen cap attached) So I assume that the segmentation should be fine. It was a false alarm of freeview yesterday.

I will let you know if I saw the same problem which is reproducible again.

Best, Chao

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ruopeng Wang Sent: Tuesday, 26 June 2012 10:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] is it a bug of freeview? or wrong segmentation?

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

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