Hi HweeLing, I think something like: mri_vol2vol -mov <input> -targ <template> -o <output> -interp nearest should work. As Doug says, you should use the aparc+aseg.mgz as your input. Use your MNI template as your target, and call your output whatever you want. Be sure to use the nearest neighbor interpolation method. This will put your whole aparc+aseg into MNI space, and then the label for STS is 1030 and 2030.
Hope that works. Jenni On Tue, Sep 16, 2008 at 9:05 AM, Hwee Ling Lee < [EMAIL PROTECTED]> wrote: > Hi, > > I'm re-posting a question. > > Pardon my ignorance. > > How do I use this mri_vol2vol command? I tried to follow the notes, > however, > I'm not quite sure, hence I was not able to write a ROI mask. > > Cheers, > HL > > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Doug Greve > Sent: 12 September 2008 18:10 > To: Bruce Fischl > Cc: freesurfer@nmr.mgh.harvard.edu; Hwee Ling Lee > Subject: Re: [Freesurfer] freesurfer > > You can also skip the 1st two steps and just convert aparc+aseg.mgz to > MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then > look for voxels with values 1030 (left STG) or 2030 (right STG). > > doug > > Bruce Fischl wrote: > > > Hi HweeLing, > > > > I think the aparc.a2005s has the STS labeled in it, so you should > > already have what you need in individual space. You could use > > mri_annot2label, mri_label2vol and mri_vol2vol to transform this into > > MNI if you need to. > > > > cheers, > > Bruce > > > > > > > > On Fri, 12 Sep 2008, Hwee Ling Lee wrote: > > > >> > >> Hi All, > >> > >> I was looking for methods to create a superior temporal sulcus > >> mask (upper and lower boundary). > >> > >>> From my understanding, Freesurfer does a pretty good job in labeling > >>> the > >> > >> sulcus, hence I was wondering if there are possible ways to write the > >> particular ROI as a mask image for each individual subject, and > >> preferably > >> to be in the MNI space or if not, at least in the native space. > >> > >> Thank you. > >> > >> Best wishes, > >> HweeLing > >> > >> > >> > >> ----------------------------------------------------------------------- > >> Hwee Ling, Lee > >> Max-Planck Institute for Biological Cybernetics > >> Cognitive Neuroimaging > >> Spemannstrasse 41 > >> 72076 Tuebingen > >> Germany > >> Tel: +49-70701-601-1785 > >> Fax: +49-7071-601-616 > >> [EMAIL PROTECTED] > >> [EMAIL PROTECTED] > >> http://www.kyb.mpg.de/~hweeling > >> ----------------------------------------------------------------------- > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Jenni Pacheco, MA Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: [EMAIL PROTECTED]
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