Doug, thanks
So, is this a correct sequence:

Im extracting thickness measures from VBM contrasts generated by FSL VBM analysis (this is 2X2X2):
 
1. To convert VBM contrast file to a binary mask:
 
mri_binarize --i vbmcontrast.nii.gz --o vbmmask.nii --min 0.95 --max 1 (for fsl vbm generated corrp maps, where values are stored as 1-p, min 0.95 identifies all voxels with p less than 0.05)
 
2. to check if this mask lies in appropriate place on fsaverage image:
 
tkmedit -f fsaverage/mri/T1.mgz -overlay vbmmask.nii -fthresh 0.5
 
3. to register groupaverage  with fsaverage
fslregister --s fsaverage --mov groupaverage/mri/T1.mgz --reg threshreg.dat
 
4. to view it on the fsaverage  volume
 
tkmedit fsaverage T1.mgz -overlay vbmmask.nii  -overlay-reg threshreg.dat fthresh 0.5 -surface lh.white -aux-surface rh.white
 
5. to map it on the fsaverage SURFACE
 
mri_vol2surf  --mov $SUBJECTS_DIR/vbmmask.nii --reg $SUBJECTS_DIR/threshreg.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.masked.mgh  --reshape
 
6. to view it  on the surface

tksurfer fsaverage lh inflated -overlay lh.fsaverage.masked.mgh  -fthresh 1
 


But I am seeing the surface projections on completely different regions than when using FSL templates to view the VBM contrast

Cheers
Lena

On 20/08/2010 20:41, "Douglas N Greve" <greve@nmr.mgh.harvard.edu> wrote:

> You'll have to sample that mask onto the surface using mri_vol2surf with
> the --interp nearest option. You will also have to have a registration
> matrix, which will depend on where the volume came from.
>
> doug
>
> Lena Palaniyappan wrote:
>> I have a mask file which I need to overlay on the individual images of
>> a group of subjects to extract thickness values within ht mask. But
>> the mask is of dimension 2X2X2, will this be an issue?
>>
>> Thanks
>> Lena
>> _______________________________________________________
>> *Lena Palaniyappan
>> *Clinical Lecturer & Honorary StR | Division of Psychiatry (
>> University of Nottingham)
>> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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_______________________________________________________
Lena Palaniyappan
Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham)
South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH

This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham.

This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.