Dear Eelke,

I am so sorry for my late response.
Thanks a lot for your previous answers! 
So in summary, if you have symmetrical effects when using only —useReconMNI it would be good to run the analysis additionally with —useRigidAlign. If the results disappear this means that the first results were actually only pose effects. Am I right with this assumption?
In this case it makes me wonder why the combination (—useReconMNI —useRigidAlign) is not set as the default setting. I think that most researchers are interested in shape not pose differences. 

Thanks a lot for your help!

All the best,

Sarah

> On Mar 15, 2017, at 5:03 PM, Eelke Visser <[log in to unmask]> wrote:
> 
> Hi Sarah,
> 
> Yes, that's right. There could still be an additional effect of shape on top of the difference in pose however, so in such a situation it would be good to try the analysis with --useRigidAlign too.
> 
> Best,
> Eelke
> 
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Sarah Hirsiger
> Sent: 15 March 2017 13:27
> To: [log in to unmask]
> Subject: Re: [FSL] FSL FIRST use --useRigidAlign?
> 
> Dear Eelke,
> 
> Thanks a lot for your quick and helpful response. I hope you don’t mind me asking another question for my understanding.
> In a former post you state that if you see a symmetric effect between your groups, this could rather be caused by pose than the structures size. This means when using only —useReconMNI and you see e.g., a positive effect for group1 (greater shape displacement) on the medial side of the structure and a positive effect for group2 on the lateral side of the same structure (let’s say right Ncl. Accumbens), this is probably caused by pose?
> 
> Thank you for your efforts! 
> 
> Best,
> 
> Sarah
> 
>> On Mar 14, 2017, at 10:05 PM, Eelke Visser <[log in to unmask]> wrote:
>> 
>> Dear Sarah,
>> 
>> You are absolutely right that --useReconMNI partially removes pose from the segmentations. The affine MNI registration used for this is estimated using a subcortical mask, and this means that pose of the entire complex of subcortical structures (plus brainstem) is removed, but not the relative pose of the individual structures. The latter type of variations in pose can be removed with --useRigidAlign.
>> 
>> Hope that helps!
>> 
>> Best,
>> Eelke
>> 
>> 
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Sarah Hirsiger
>> Sent: 14 March 2017 17:56
>> To: [log in to unmask]
>> Subject: [FSL] FSL FIRST use --useRigidAlign?
>> 
>> Dear FSL-Experts
>> 
>> I anticipate to conduct a FSL-FIRST analysis and was screening the FSL mailing list for advice.
>> 
>> Based on the FIRST UserGuide you could either reconstruct the meshes in the native space of the images with [--useReconNative --useRigidAlign ] or in MNI space with [—useReconMNI].
>> 
>> Additionally, there is noted that to remove pose from the meshes you should use —useRigidAlign (with either --useReconNative or --useReconMNI)
>> 
>> Does this mean that if I am not interested in pose of a structure I should run --useReconMNI WITH --useRigidAlign? 
>> This seems not straight forward to me as I would assume that the transformation to MNI space would already take care of this?
>> 
>> Thanks a lot for your help
>> 
>> Sarah