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: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 16 September 2008 22:51 To: Hwee Ling Lee Cc: freesurfer@nmr.mgh.harvard.edu; '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 fischl@nmr.mgh.harvard.edu 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: 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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 17 September 2008 15:32 To: Hwee Ling Lee Cc: freesurfer@nmr.mgh.harvard.edu; '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: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 16 September 2008 22:51 To: Hwee Ling Lee Cc: freesurfer@nmr.mgh.harvard.edu; '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 fischl@nmr.mgh.harvard.edu 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: 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 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
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 -
Hwee Ling Lee