Hi Bruce, Thanks for prompt reply. I shall try it tomorrow. Cheers, HweeLing
On Tue, 16 Sep 2008 16:51:23 -0400 (EDT) Bruce Fischl <[EMAIL PROTECTED]> wrote: > Hi HweeLing, > > you can use mri_extract_label aparc+aseg.mgz <label> <output volume> > > then the command line Jenni posted before to transform it to MNI space (or > you can try giving the talairach.xfm to mri_extract_label with -t, but I'm > not positive that works) > > cheers, > Bruce > > > > On Tue, 16 Sep 2008, Hwee Ling Lee wrote: > > > > > Hi, > > > > I wanted to write out a mask image for left and right STS as Analyze > format file. > > Using this, I plan to plot the parameter estimates along the STS, > posteriorly to anteriorly. > > I know this is an unusual way of doing things, however, I thought this > might be best suited to customize each STS mask for individual subjects as > many studies have shown differences in STS morphology. > > > > Thanks, > > HweeLing > > > > > > On Tue, 16 Sep 2008 15:44:11 -0400 (EDT) > > Bruce Fischl <[EMAIL PROTECTED]> wrote: > >> can you tell us exactly what you would like to do with it? > >> On Tue, 16 Sep 2008, Hwee Ling Lee 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 > >>>> > >>>> > >>> > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > Hwee Ling, Lee > > > > PhD student > > http://www.kyb.mpg.de/~hweeling > > Max-Planck Institute for Biological Cybernetics > > NWG Noppeney > > Spemannstr 41 > > 72076 Tuebingen > > > > > > Hwee Ling, Lee PhD student http://www.kyb.mpg.de/~hweeling Max-Planck Institute for Biological Cybernetics NWG Noppeney Spemannstr 41 72076 Tuebingen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
