Dear Bruce,
   I try to extract freesurfer cortical thickness valunes for a ROI defined in volume space (avg152T1.nii.gz). I try a lot and have extracted the values successfully now. Thank you very much. I suggest the experts can change opition "--reshape" of mri_vol2surf and mri_surf2surf into "--noreshape".  If I use opition of reshapre, it always report the errors of dimension. 

Thank you 

Wang Kangcheng
From: Bruce Fischl
Date: 2014-06-16 21:04
To: kangchengwang0808@gmail.com
CC: freesurfer
Subject: Re: [Freesurfer] Problem of VolumeRoiCorticalThickness
Hi Wang
 
you can't change the atlas that way. We extract a ton of information and
store it in what we call an atlas, and what we require isn't in the
harvard-oxford one. What are you trying to achieve?
 
cheers
Bruce
 
 
On Mon, 16 Jun 2014,
kangchengwang0808@gmail.com wrote:
 
> Dear Bruce,
>
> Now, I change the standard atlas to avg152T1.nii.gz which was included in
> the FSL and make a mask of superior frontal gyrus  (Harvard-Oxford Cortical
> Structural Atlas). I can map the ROI-mask to the fsaverage surface to create
> an fsaverage-ROI surface overlay. But when I map one subject thickness data
> to the fsaverage subject  using the following command:
>
>  mri_surf2surf --s s12129 --trgsubject fsaverage --hemi lh --sval s12129/sur
> f/rh.thickness --tval ~/Desktop/mask/rh.thickness.fsaverage.mgh --reshape
>
> it said:
>
>  Reading source surface reg /Users/wangkangcheng/Desktop/dataplus_60/s12129
> /surf/lh.sphere.reg
> Loading source data
> ERROR: dimension inconsistency in source data
>        Number of surface vertices = 146027
>        Number of value vertices = 145656 
>
> How could solve this problem?
>
> Thank you  
> Wang Kangcheng
>
>
>
>
 
 
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