Hi Jing, I'm reposting to the group in case someone else has any suggestions. I've answered some of your questions below

1) all of our outputs are "conformed" meaning that they are resampled to 1mm3 256^3. To convert back to native anatomical space search for "native" on our wiki.

2) Don't know

3) Don't know

doug

Huo, Jing wrote:

Hi Douglas,

Thanks a lot for your reply!!! I am doing brain tumor segmentation with voxel-based classification. We have images from all difference scanners. To have good performance in the training stage, I need to normalize the intensity into the same range... And after segmentation, I need to compare the ground truth and the automated results. I don't have a choice here...:(

-Jing ________________________________________ 发件人: Douglas N Greve [greve@nmr.mgh.harvard.edu] 发送时间: 2010年10月14日 15:12 收件人: Huo, Jing 抄送: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] Problem with intensity normalization

Jing, why are you running these commands by hand instead of just running recon-all? These are very complicated steps and don't lend themselves to running by hand.

doug

Huo, Jing wrote:

...

Hi,

I have a problem with using mri_normalize for intensity normalization for T1w+contrast 3D volumes.

What I ran: mri_convert t1.hdr t1.mgz mri_normalize -g 1 t1.mgz t1_norm.mgz mri_convert t1_norm.mgz t1_norm.hdr

(1) The first problem is that all volumes are 256*256*256 as output. Why are there dummy slices? Is there an automatic way to get rid of the dummy slices?

(2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I was wondering whether this comes from the spatial registration, but it is wierd coz the rest 2/3 of the cases are pretty OK visually. Anyone has similar experience before? That would be very helpful. Thanks.

(3) For 4 cases, the brain white matter was normalized to 59 instead of 110. I dunno why...

Thanks! I will really appreciate if anyone could help here!

Best, Jing

IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

---

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

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.

IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.