I think in freeview the syntax would be:
freeview -f lh.inflated:label=lh.your_ROI.label
cheers Bruce
On Tue, 16 Jul 2013, Yang, Daniel wrote:
Hi Bruce,
Sorry for so many responses. I figured it out that I can visualize it using tksurfer.
Besides this, can I visualize it in freeview, CARET, or some other tools? My goal is to display the ROI on a fsaverage inflated surface.
If it can be done in freeview, could you give me some instruction? In freeview, I found that I can only load ROI after I load a volume, but not after I load a surface.
Thanks! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 7/16/13 10:14 AM, "Yang, Daniel" yung-jui.yang@yale.edu wrote:
Hi Bruce,Thanks so much! So I ran the following and obtained all the DK ROI labels.
mri_annotation2label --subject fsaverage --hemi rh --outdir
<my_output_dir>
Then, I am wondering how I can use the label files. For example, can I overlay it on a brain in fslview?
The label file has many lines. Could you suggest what document I can read in order to interpret it? One of them is like, "1530 47.244 -41.285 -1.841 0.0000000000".
Thanks for your help! Daniel
-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 7/16/13 9:32 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Danielyou could use the DK annotation of the fsaverage brain, which I think we supply. The atlas itself is a compilation of multiple statistics and not easily visualizable (except for the prior probability I guess).
cheers Bruce
On Tue, 16 Jul 2013, Yang, Daniel wrote:
Hi Bruce,I am sorry, I mean, is there a DK atlas on a standard template brain (like MNI 152)? sorry, I don't know how DK atlas works. Is it a probabilistic atlas, or dependent on the exact folding pattern of the unique individual? (I guess it's the latter). I'd like to generate a ROI brain mask for a specific region on the DK atlas, independent of the individual I ran. Having said so, I guess I can just run recon-all on a MNI 152 brain, so that I can get the ROI maps. Thanks, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 7/15/13 8:43 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel sorry, can you clarify? The DK atlas is estimated on every brain that you run recon-all on and stored in the label directory. Is that what you want? cheers Bruce On Mon, 15 Jul 2013, Yang, Daniel wrote:
Dear FreeSurfer Expert, I would like to draw the specific ROI of the DK atlas (not specific individual, but this ROI in general). I'm wondering how this ROI can be extracted/created as a mask so that I can draw it on the brain using some software? Could you please advise? Thanks a lot, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.