Hi Bruce, I was able to write the gyrus from the labels, however, when I tried to write one of the sulcus (1180), there was nothing in the image. Would I have to use a different input volume? Currently, I'm using aparc+aseg.mgz.
Thanks, HweeLing -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl Sent: 17 September 2008 15:32 To: Hwee Ling Lee Cc: [email protected]; 'Doug Greve' Subject: RE: [Freesurfer] freesurfer they are listed in $FREESURFER_HOME/FreeSurferColorLUT.txt cheers, Bruce On Wed, 17 Sep 2008, Hwee Ling Lee wrote: > Hi Bruce, > > Thanks for the advice. > It works well. > I was wondering if there's any way I could check what values of the label > correspond to a particular brain region. > Thanks. > > Cheers, > HL > > > > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl > Sent: 16 September 2008 22:51 > To: Hwee Ling Lee > Cc: [email protected]; 'Doug Greve' > Subject: Re: [Freesurfer] freesurfer > > 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: [email protected]; 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 >>>>>> [email protected] >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> [email protected] >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> 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 >> >> >> > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
