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 < hwee-ling.lee@tuebingen.mpg.de> 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: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] 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 hwee-ling.lee@tuebingen.mpg.de hweeling.lee@gmail.com http://www.kyb.mpg.de/~hweeling
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Jenni Pacheco