Hi Javier,
Sorry for not responding earlier - I was away for a few days. As your image appears to be quite inhomogeneous, running it through fast (with -B -t 2 options) to remove the bias field might improve things. The bias corrected output from fast is called <input image>_restore.
If that doesn’t help, some screenshots with the crosshair in the same location for both images would help me to see where the registration errors are.
Cheers,
Eelke
> On 19 Jun 2015, at 05:35, Javier Sanz Perez <[log in to unmask]> wrote:
>
> Hi Eelke,
>
> Sorry, you are right, it's hard to see. I attach two screenshots more. I rewrote the header of the anatomic images to multiply the spatial resolution by 10, in order to improve the results of BET and other tools. The template remained untouched.
>
> Thanks for your help,
> Regards,
>
> Javier
>
> 2015-06-18 23:36 GMT+02:00 Eelke Visser <[log in to unmask]>:
> Hi Javier,
>
> I still find it a bit hard to see what is going on as your scan is behind the atlas image. Would you mind adding a screenshot with the actual scan on top?
>
> Thanks,
> Eelke
>
>
>
>> On 17 Jun 2015, at 23:19, Javier Sanz Perez <[log in to unmask]> wrote:
>>
>> Hi Eelke,
>>
>> Thank you for your answer. I ran flirt -in ${anatomic_dir}/anatomic_brain.nii.gz -ref ${template} -dof 6 -out ${anatomic_dir}/anatomic_tostandard.nii.gz -omat ${anatomic_dir}/anatomic_tostandard_transform.mat.
>> I attach two screenshots: one with 6 degrees of freedom and the other with 12 degrees of freedom.
>>
>> Best regards,
>>
>> Javier
>>
>>
>> 2015-06-18 3:27 GMT+02:00 Eelke Visser <[log in to unmask]>:
>> Hi Javier,
>>
>> The anisotropy is not necessarily a problem for FLIRT, but it is a bit hard to guess what is going on without seeing the images. Would it be possible to share some screenshots along with the options you used when running it?
>>
>> Cheers,
>> Eelke
>>
>>
>>> On 17 Jun 2015, at 10:48, Javier Sanz Perez <[log in to unmask]> wrote:
>>>
>>> Hi everyone,
>>>
>>>
>>>
>>> I’m having problems trying to register anisotropic anatomic rat images (0.2x0.2x1 mm3) to an isotropic template (1.25x1.25x1.25 mm3) with FLIRT, 6 and 12 DoF. The resulting image is not properly registered to the template.
>>>
>>>
>>>
>>> I was wondering if the problem was due to the high anisotropy of the images (1/0.2=5) compared to the isotropy of the template. How can the registration improve?
>>>
>>>
>>>
>>> Thank you,
>>>
>>> All the best,
>>>
>>>
>>>
>>> Javier
>>>
>>
>>
>> <FLIRT_6dof.png><FLIRT_12dof.png>
>
>
> <6dof_template_behind.png><12dof_template_behind.png>
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