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 mailto: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 mailto: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 <mailto:cherif@mit.edu> "Live as if this were your last day. Learn as if you'll live forever" Ghandi -------------------------------------------------------------------------------------------
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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.eduwrote:
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.eduwrote:
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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 Centergreve@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
freesurfer@nmr.mgh.harvard.edu
-
Cherif Sahyoun -
Doug Greve