yes, it should doug On 12/14/2012 07:43 PM, octavian lie wrote:

Dear Doug, Thank you for your suggestions, to be more clear, the original preresection volume was in old analyze format (hdr/img), and was already processed through freesurfer, so I have pre.mgz instead of pre.img. I do not have the pre.img any more, but pre.mgz. Do the formulas still apply (with changing nii to img)? Also, the postresection volume is .img. Thank you, Octavian.

On Thu, Dec 13, 2012 at 11:52 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

On 12/12/2012 09:42 AM, octavian lie wrote:
> Dear All,
> Excuse the basic nature of these quetions. I coregistered 2 analyze
> volumes in SPM (pre and post resection MR scans for same
patient) with
> cost function masking. I imported the preresection scan in
Freesurfer,
> and processed it with recon -all.
> 1) What transform matrices should I multiply the postresection
scan to
> get it in the FS space in alignment with the processed preresection
> MR, and where do I find them?
If the two volumes are in alignment, then you can run
mri_vol2vol --mov post.nii --targ pre.nii --regheader --o
post-in-pre.nii

To check that FS thinks that they are in alignment, you can run
tkregister2 --mov post.nii --targ pre.nii --regheader --reg junk.dat


> 2) Once in FS, how do I crop/mask the posteresection volume using
> saggittal, coronal or axial planes of my choosing? (I am
interested in
> generating a small cube containing the posteresection volume, then
> extracting the postresection volume itself by intensity
threshold (CSF
> vs surronding cavity wall brain) and masking with preresection
MR pial
> surface laterally).
You can use --crop and --cropsize options in tkmedit
  mri_convert --crop 1 2 3 --cropsize 100 120 130 input.nii output.nii
> Please advise,
> Octavian.
>
>
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