Hello, Bruce,
I'd like to send you this subject data, could you please let me know where I can drop it?
Thanks! Guang
Date: Wed, 31 Mar 2010 08:44:42 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FW: how to modify the wm.mgz
Hi Guang,
yes, it looks like the segmentation didn't do a great job on your data. if you send us the orig.mgz we'll take a look (or the individual runs 00?.mgz in the orig dir if you have more than one). You could copy the SPM results to wm.mgz and proceed from there I think, or you can use the expert options to correct the intensity thresholds
cheers, Bruce
On Tue, 30 Mar 2010, Guang Zeng wrote:
Hello, Bruce,
Thanks a lot for your reply, I reload the pictures with surface overlayed.
So,
fig. 1 is the segmentation results and surface overlayed to the original volume fig.2 is the wm.mgz fig.3 is the surface overlayed to wm.mgz fig.4 is the segmentation results overlayed to the wm.mgz fig.5 is the surface overlayed to the wm mask I created using SPM5 fig.6 is the segmentation results overlayed to the wm mask I created using SPM5
In fig.4, we can see part of the wm mask were classified as gm after the FreeSurfer analysis was done. It is quite different from what I see when I load the wm.mgz and the segmentation results of the bert subject from FreeSurfer tutorial. In bert subject, the wm.mgz quite match with the final segmentation results.
So I am wondering if I used my own wm.mask to replace freesurfer built wm mask, could I get a better result?
Thanks! Guang
Date: Mon, 29 Mar 2010 20:48:20 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: how to modify the wm.mgz
Hi Guang,
it's hard to tell without looking at the surfaces. I don't think a wm mask will help. You could try using the expert options to change the intensity bounds that are automatically detected by mri_segment and mris_make_surfaces.
cheers Bruce On Mon, 29 Mar 2010, Guang Zeng wrote:
Hi there,
Recently, I use FreeSurfer analyze a clinic data, the result show a very thin cortex layer, (see figure. 1). I load the wm,mgz (see figure.2), and then overlay the segmentation results, (see figure. 3). As you can see, part of wm.mgz around the wm mask boundary are classified as gm, I guess this is because of partial volume.
My question is if I use a better wm mask to replace freesurefer's brainmask (see figure. 4), could I get a better result?
Thanks! Guang
Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:W...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:W...
_________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:W...