Re: [Freesurfer] result is L-R fliped in native space

2013-10-22 Thread wen.zhang55 
Dear doug:

I overlaped the transformed vol ROI to the original T1 image, both in native 
space, then surprisingly found out that lh labeled ROI was on the right 
hemisphere but contained the exact lh sulcus or gyrus information. I converted 
the spacific label to ROI based on white/grey boundry, so I can confirmed the 
quality of my result with the help of morphormetric information of that boundry 
just by eyes.  

best,
cowen

2013-10-22



wen.zhang55



发件人：Douglas N Greve 
发送时间：2013-10-22 23:04
主题：Re: [Freesurfer] result is L-R fliped in native space
收件人："freesurfer"
抄送：

How are you determining that they are lr flipped? 

On 10/21/2013 11:18 PM, wen.zhang55 wrote: 
> Dear Freesurfer： 
> I am now working in converting cortical labels from freesurfer to  
> volumetric masks. First i gained the registration matrix by  
> bbregister, then applied those matrix to tranform ROI labels into  
> native space using label2vol. However, when i got the final .NII  
> results, both of them turn out to be L-R fliped. (left ROI on the  
> right hemisphere). From my understanding, freesurfer will automaticly  
> recognize the head direction of the original T1 images and my original  
> T1 data contains the flip information due to the way we scaned. 
> So why this happen? By the way, the recon-all results did good. 
> Thank you very much! 
> best, 
> Cowen 
> 2013-10-22 
> ---- 
> wen.zhang55 
> 
> 
> ___ 
> Freesurfer mailing list 
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

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MGH-NMR Center 
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[Freesurfer] result is L-R fliped in native space

2013-10-21 Thread wen.zhang55 
Dear Freesurfer：

I am now working in converting cortical labels from freesurfer to volumetric 
masks. First i gained the registration matrix  by bbregister, then applied 
those matrix to tranform ROI labels into native space using label2vol. However, 
when i got the final .NII results, both of them turn out to be L-R fliped. 
(left ROI on the right hemisphere). From my understanding, freesurfer will 
automaticly recognize the head direction of the original T1 images and my 
original T1 data contains the flip information due to the way we scaned. 

So why this happen? By the way, the recon-all results did good.
Thank you very much!   

best,
Cowen 

2013-10-22



wen.zhang55___
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[Freesurfer] problem with surface area regression

2013-06-24 Thread wen.zhang55 
Dear Freesurfer,   
   
I have checked the mail list, none could answer my problem.   
I added up the value of all vertxes in the .area or .area.pial files, find that 
brain size did not contribute much to that vertex-sum. However, some experiment 
used total brain volume as a regreesion coefficient to remove brain size 
effect. In these case, with the comparison of surface area in vertex-to-vertex, 
is it proper to use the above vertex-sum as the regression coefficient to 
remove different brain size?
Thank you very much!   
   
Cowen   
   
2013-06-24   
   
   
   
wen.zhang55   

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