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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