Hello, Doug,

Thanks a lot for your reply.
What you said is correct. I saw those non-connected or non-contiguous labels which show as 'No label' when I import the annotation file.

Two questions:
1. If I want to use my own annotation files to create own surface atlas, all the vertices  stored in my annotation files should have a label?

2. What is the label for those vertices shown as 'No label'? Or they will not be written in the annotation file?

Thanks!
Guang



> Date: Wed, 16 Dec 2009 13:12:59 -0500
> From: greve@nmr.mgh.harvard.edu
> To: freesurfer_zg@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] a question about mris_ca_train
>
> You can use mri_vol2surf with the --interp nearest option to sample your
> volume segmentations onto the surface. You can then use mris_seg2annot
> to convert this segmentation directly to an annotation, then use
> mri_annotation2label to convert the annotation into a set of labels.
> Nothing here guarantees that labels will be connected or contiguous nor
> is it sure that all vertices on the surface will be labeled.
>
> doug
>
> Guang Zeng wrote:
> > Hi, there,
> >
> > Recently, I sent sseveral emails to you to ask same kind of question
> > about building our own template and atlas.
> > Thanks a lot for your quick reply, they helps me a lot.
> >
> > Currently, I still have a question about building our own atlas using
> > mris_ca_train, sorry to bother you again.
> >
> > We have a surface labeling atlas in our lab, we'd like to use this
> > atlas instead of using FS's desikan_killiany.2007-06-20gcs.
> > It is kind of difficult for us to load every subject in our training
> > set to tksurfer, and manually label each ROI based on our ATLAS.
> >
> > What we try to do is:
> > 1. Send each subject in the training set to our toolbox which will use
> > our atlas to do surface labeling. For each subject it will output a
> > file just like
> > wmparc.mgz in FS, but it is NIfTI file.
> >
> > 2. Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc
> > files.
> >
> > 3. Find a method to get my ?h. mylabels. annot files, and use
> > mris_ca_train to build a new atlas.
> >
> > First of all, do you think what I try to do is reasonable?
> >
> > If yes, I know I need to get the FS .label files for each ROI, then I
> > can call mris_label2annot to get ?h. mylabels. annot files.
> >
> > But how can I get the FS .label files for each ROI from our toolbox
> > output ROI labeled NIfTI file?
> >
> > These qurstions trouble me for a long time, your help are really
> > appreciate.
> >
> > Thanks a lot!
> > Guang
> >
> >
> >
> >
> >
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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