Hey Doug,

A follow-up:
Is there a reason mri_label2vol would "work" better when registering from fsaverage to a high res T1 than to the MNI152 or even to the fsaverage volume?
If I run
mri_label2label --srclabel $label --srcsubject fsaverage --trgsubject $subject --trglabel $label --regmethod surface --hemi rh
mri_label2vol --label $SUBJECTS_DIR/$subject/label/$label --temp $SUBJECTS_DIR/$subject/mri/brain.mgz --proj abs -2.5 0 .1 --o $subject/dti/T1_ROIs/$label.proj2.5.nii --subject $subject --hemi lh
then the label lies beautifully on the grey-white boundary and follows the gyral pattern closely
See for ex in
fslview /space/monday/users/cherif/T1_brain.nii.gz /space/monday/users/cherif/lh.IFS.label.proj2.5.nii -l Green

However if I try
mri_label2vol --label $label --temp $SUBJECTS_DIR/fsaverage/mri/brain.mgz --proj abs -2.5 0 .1 --o ${label}_vol.nii --subject fsaverage --hemi lh
or
mri_label2vol --label $label --temp MNI_brain.nii.gz --reg $FREESURFER_HOME/average/

mni152.register.dat --proj abs -2.5 0 .1 --o ${label}_vol.nii --subject fsaverage --hemi lh

then I get what you can see with
fslview /space/monday/users/cherif/fsaverage_brain.nii.gz /space/monday/users/cherif/lh.IFS.label_vol.nii -l Green

or
fslview /space/monday/users/cherif/MNI_brain.nii.gz /space/monday/users/cherif/lh.IFS.label_mni.nii -l Green

i.e. the label now lies somewhat away from the grey-white boundary and circles around several folds instead of following each one.

Is this just because the targeted brains are smoothed averages instead of high-res individual T1s?
My plan is to run probabilistic tractography in a common template brain based on functional ROIs drawn on fsaverage, but I am worried my seeds my fall too approximatively following mri_label2vol.

Thoughts? recommendations?
Thanks,
Cherif

------------------------------------------------------------------------------------------
Cherif P. Sahyoun HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
cherif@mit.edu

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
-------------------------------------------------------------------------------------------

On Mon, Sep 15, 2008 at 12:14 PM, Doug Greve <greve@nmr.mgh.harvard.edu> wrote:

yep, you can use that one.
Cherif Sahyoun wrote:
Thx Doug!
What should I use as --temp?
I have the MNI152 that fsl uses, but I'm not sure it's the one you used (orientation-wise) to create the reg file.

------------------------------------------------------------------------------------------
Cherif P. Sahyoun HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
cherif@mit.edu

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
-------------------------------------------------------------------------------------------
On Fri, Sep 12, 2008 at 12:08 PM, Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
You can use mri_label2vol and spec $FREESURFER_HOME/average/mni152.register.dat as the registration file.

Cherif Sahyoun wrote:
Hi,

I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152 volume. Any ideas on how to do it?
Usually I'd mri_label2label and then mri_label2vol, but I don't think there is a surface version of MNI152, is there?

Thanks!
Cherif
------------------------------------------------------------------------------------------
Cherif P. Sahyoun HST-MEMP

Developmental Neuroimaging of Cognitive Functions

C: 617 688 8048
H: 617 424 6956
cherif@mit.edu

"Live as if this were your last day. Learn as if you'll live forever"
Ghandi
-------------------------------------------------------------------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

    
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting