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(a)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(a)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(a)itsa.ucsf.edu wrote:
>>
>>> This are the steps I use fsl_register_new:
>>> 1) mksubjdir AD1378
>>> 2) mri_convert xAD1378-T1.img AD1378/mri/orig
>>> 3) 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
>>
>
>
>
>