Just to add one more subtle comment. The --useReconMNI, does not
necessarily reflect purely differences in brain, probably more of a
general subcortical size and position. This is because the linear
transform used was that which was put into FIRST (from first_flirt), which
uses a subcortical + ventricles mask in its second stage of registration.

cheers,

brian

> Dear Arash,
>
> There is a difference between these options, as the useScale option
> removes
> all average scaling information from that structure.  Hence if it does not
> scale
> exactly with brain size then the two scalings will be different.
> Particularly, if you
> had a diffuse atrophy (scaling) of one structure, independent of brain
> size, then
> the --useScale option would tend to remove that atrophy.  Hence it is much
> more
> common to want to normalize by the brain size instead, and therefore to
> use the
> --useReconMNI option.
>
> Hope this is clear.
> All the best,
>       Mark
>
>
> On 14 Jun 2011, at 14:22, Arash Nazeri wrote:
>
>> Dear Mark,
>>
>> Thank you very much. Could this be resolved by accounting for global
>> thalamic changes across subjects with adding --useScale option to
>> --useReconNative? As brain size most likely affect global measures of
>> sucortical nuclei.
>>
>> Many thanks,
>> Arash
>>
>> On Tue, Jun 14, 2011 at 3:51 AM, Mark Jenkinson <[log in to unmask]>
>> wrote:
>> Dear Arash,
>>
>> I hope you only used the --useRigidAlign with the --useReconNative
>> option.
>> They should be used together but the --useReconMNI should be used on its
>> own.
>>
>> As the MNI-space reconstruction puts the image into MNI space, it
>> normalizes
>> for brain size as part of the process, whereas the native-space
>> reconstruction
>> does not.  So the most likely thing is that you are seeing a difference
>> due to
>> brain size changes which is being normalized away in the --useReconMNI
>> option.
>>
>> It might be worth checking to see if there is a systematic brain size
>> change
>> amongst your subjects which would support this interpretation.
>>
>> All the best,
>>        Mark
>>
>>
>> On 14 Jun 2011, at 04:46, Arash Nazeri wrote:
>>
>> > Dear Mark,
>> >
>> > As it has been recommended on FIRST's documentation webpage, we tried
>> FSL vertex analysis using both --useReconNative and --useReconMNI
>> flags along with --useRigidAlign. However, --useReconNative yielded a
>> lot of significant regions on both left thalamus and left pallidum
>> while --useReconMNI yielded none.
>> > Does this mean that our findings are in fact spurious?
>> >
>> > Thanks,
>> > Arash
>>
>
>