Thanks very much Mark...
Best,
Lance
On Wed, Jul 5, 2017 at 4:31 AM, Mark Jenkinson
<[log in to unmask]> wrote:
> Hi,
>
> Yes, if your image does not cover the required structure then FIRST will fail.
> The registration part of it may be fine, but the lack of boundary in part of the structure will cause major errors. So in that case I would exclude that subject.
>
> All the best,
> Mark
>
>
>> On 19 Jun 2017, at 19:12, Lance Stevens <[log in to unmask]> wrote:
>>
>> FSL experts,
>>
>> Of 19 T1 images representing a patient group that can not be rescanned, two T1s are truncated in the z-plane: one is cut-off at Z -48 in native space and the other at Z -73 in native space. It may be that the T1 cut-off at Z -48 will produce registration errors.
>>
>> Part of the planned analyses involves FSL-FIRST hippcampal volume and vertex analyses. My concern is that the T1 cut-off at -48 in native T1 space seems to be about -20 in MNI152 space; using fsleyes, and at Z -20 in MNI space, this seems to truncate a small inferior portion of the hippocampus. As such I would expect this subject’s T1 would generate registration errors in FIRST and should not be included.
>>
>> Unless I’ve miscalculated the MNI equivalent to -48 native space, it seems prudent to not include this subject, correct?
>>
>> Best,
>> Lance
>
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