I have a image xAD1378-T1.img with spm format. after I converted it to COR with mri_convert xAD1378-T1.img AD1378/mri/orig and run FLIRT as Xiao suggests, I found that the anterior and posterior parts of tranformed image was inversed. Xiao thinks it is due to mri_convert, Does anyone know how to fix it? thx,
Antao
---------- Forwarded message ---------- From: Xiao Han xhan@nmr.mgh.harvard.edu Date: Mon, 22 Aug 2005 16:03:46 -0400 (EDT) Subject: Re: [Freesurfer] coregistration
It has nothing to do with fsl_register. It's because of the conversion from .img to COR format. That's why I suggested you to convert all your data to COR or mgz first before processing.
The reason is because Analyze store data in an anterior-to-posterior fashion, but when mri_convert read the data, it assumed posterior-to-anterior (due to a missing .mat file).
I dont know how to fix that. You can send an email to freesurfer list.
-Xiao
On Mon, 22 Aug 2005, antao@itsa.ucsf.edu wrote:
After I run: fsl_register_new -i AD1378/mri/orig -r average_305.mnc -o AD1378/tmp/orig -dof 9 -cost corratio -ltamat AD1378/mri/transforms/talairach.lta
I check the tranformation with: tkmedit -f average_305.mnc -aux AD1378/tmp/orig. I find that the anterior and posterior parts of the image AD1378/tmp/orig are inversed. Do you know why?
When I run fsl_register_new with images .img before converting to COR, the result was good.
Antao
n Mon, 22 Aug 2005 14:16:34 -0400 (EDT) Xiao Han wrote:
On Mon, 22 Aug 2005, antao@itsa.ucsf.edu wrote:
This are the steps I use fsl_register_new:
- mksubjdir AD1378
- mri_convert xAD1378-T1.img AD1378/mri/orig
- fsl_register_new -i AD1378/mri/orig -r average_305.mnc -o
AD1378/mri/orig -dof 9 -cost corratio -ltamat AD1378/mri/transforms/talairach.lta
I have a question here. Should I replace orig when I run
fsl_register_new
or I should choose different filename?
No, you shouldn't replace the original orig. Use a different name for the -o option.
After I run fsl_register_new, I should replace talairach.xfm in
recon-all
script to talairach.lta and run recon-all. Do I need add -notalairach in stage1?
Right, you can replace talariach.xfm with talairach.lta. Also specify -notalairach when you run recon-all.
-Xiao