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Hi ,

Thank you for your reply , From what I understand ,

1) we'd better select -T unless all the subjects are young children in 2rd step .Why ? Is it just for saving time ? Which one is better result compared with -n ? Are there other circumstances in which we select -n ?

2) we'd better select -S because it derive the mean FA and skeleton from the actual subjects we have and is more accurate in 3rd step .Then in what conditions will we use -T ? Or what is the advantage of -T ？

Regards .

Shi Xin-Fa.

2014-06-27 15:33 GMT+08:00 Mark Jenkinson <[log in to unmask]>:

Hi,

> I run tbss following the user guide , and some problems confuse me .
> In 2nd and 3nd step ,there are some parameters to choose , i.e tbss_2_reg -T/-t/-n , tbss_3_postreg -S/-T.
>
> 1. I f selecting -t , then I must supply a target image ,which may not be any one of all subjects' FA images and standard template . Is it right ?

We do not recommend this option. It is really only there for people who want to use an alternative version of the FMRIB58_FA template.

> 2. If selecting -T in 2nd step , then must I use -T in 3nd step ?

No. The recommendation (as stated in the help) is -T for stage 2 and -S for stage 3.

> Or if selecting -n in 2nd step , then must I use -S in 3nd step?

This would be the recommendation.

> Is there a connection between them? I don't think so . And you ?

They are pretty much separate, although using -t and then -T doesn't really make sense.

> 3. How should I choose these parameters ?

I would follow the recommendations, as they are there for a reason.

All the best,
Mark

> Regards .
>
> Shi Xin-Fa .