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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/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
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
Hi,
Thanks for the advice. Pardon my ignorance, but I have difficulties to write the full command for mri_vol2vol. I've tried to read the help notes for mri_vol2vol, however I'm still not sure. Would this allow me to choose a particular ROI, say superior temporal sulcus, and write it out as a separate image to be used as a mask image in another program?
Thanks, HweeLing
-----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
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
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
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Hwee Ling Lee