It was version 4.50. I had to walk over to the other room to find out. ;)

 In any case, I achieved good results by including the use-mritotal flag on
the current version.

Josh



On Tue, Apr 17, 2012 at 12:00 PM, Alan Francis <alandarkene...@gmail.com>wrote:

> Hi Joshua:
>
> What version of FS 4 did you use?
>
> best,
>
> Alan
>
> On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee <jki...@ucdavis.edu> wrote:
>
>> Hi All,
>>
>> I thought I'd share my recent experiences with the newest Freesurfer v.
>> 5.10 and subcortical segmentation.
>>
>> I ran a large sample of brains using the default stream of Freesurfer v.
>> 5.10. The resulting hippocampal segmentations were extremely poor, yet on
>> the same sample of brains Freesurfer v. 4.xx did quite well.
>>
>> Using tkregister, we discovered that the hippocampus is not being
>> registered well enough. Nick Schmansky one wrote in another post on this
>> list-serve that one difference between versions is that "talairach.xfm
>> is needed to compute nu.mgz, [and] talairach stage needs to precede the
>> nu_correct stage" He suggested using -use-mritotal in the recon-all command
>> to overcome tal-check failures.
>>
>> I decided to try using -use-mritotal with this sample of my data, despite
>> tal-check not failing in the default stream. Resulting segmentations were
>> now both realistic and accurate, and near identical to those produced by
>> Freesurfer version 4.xx.
>>
>> Have others experienced poor subcortical segmentation with current
>> version of Freesurfer? I should note, that I am having this problem on
>> another sample of MPRages of very good quality. I am concerned that future
>> versions of Freesurfer will limit use of the old stream to situations in
>> which tal-check fails.
>>
>> Thanks you all.
>>  Sincerely,
>>
>> Joshua Lee
>>
>>
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