Re: [Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Douglas N Greve
If the source is the FSL standard brain, then use $FREESURFER_HOME/average/mni152.register.dat as the registration. See if that works at stage 4. Lena Palaniyappan wrote: > Doug, thanks > So, is this a correct sequence: > > Im extracting thickness measures from VBM contrasts generated by FSL >

Re: [Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Lena Palaniyappan
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

Re: [Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Douglas N Greve
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 i

[Freesurfer] Volume to surface dimension mismatch

2010-08-20 Thread Lena Palaniyappan
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 Lecture