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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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:
- 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.
- Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc
files.
- 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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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:
- 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.
- Send each subject to FS pipeline to get the ?h.sphere.reg, ?h.sulc
files.
- 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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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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Guang Zeng