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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