Dear Mark,
Thanks for the response! The reason I’m using 12 dof is because we’re using multi band, and even after reconstructing and unwarping there is considerable warping clearly visible even within a single run. Moreover, I am concatenating my data across 3 days of scanning, and I do not want parts of the brain moving in and out of voxels. The 12 dof MCFLIRT is doing a good job of correcting all of this, I just have not been able to find any quantifiable output of how much it is actually correcting.
-Rosanne
On Jul 5, 2017, at 1:31, Mark Jenkinson <[log in to unmask]> wrote:
> Dear Rosanne,
>
> Is there any reason that you are using 12 DOF for motion correction?
> This does not make a lot of sense typically (as the brain is only translating and rotating, not scaling or skewing due to motion). That is the reason that the mcflirt tool only outputs 6 DOF.
>
> All the best,
> Mark
>
>
>> On 15 Jun 2017, at 19:35, Rosanne Rademaker <[log in to unmask]> wrote:
>>
>> Hi all,
>>
>> I am currently running MCFLIRT for motion correction with 12 dof. I want to regress out my motion parameters so have included the -plots flag. However, I noticed that only 6 parameters (x-y-z and roll-pitch-yaw) are saved out. How can I save out the other 6 parameters?
>>
>> Thanks,
>> -Rosanne
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