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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
