Thanks Gwenaelle,
This is a pediatric sample, so I assume it is better to run with the -
S option ? Not a problem, I already ran it and the skeletons are all
the same now, was just checking ;-)
Best,
Naama
On Apr 21, 2009, at 9:23 AM, Gwenaëlle DOUAUD wrote:
> Hi Naama,
>
> yes, it would be valid, but I presume you don't need to rerun the
> whole 2-4 steps...
> It looks slightly "misregistered" quite likely because you ran tbss3
> with the -S option, so the mean FA and skeleton are derived for each
> of your group. The skeletons are different, but the registration
> should be the same if you have run the tbss2 step with the FMRIB58
> template.
> If so, then you don't need to run it again. You just need to run the
> tbss3 with the option -T with all your subjects in the same FA
> directory, then tbss4. Basically what you want here is a common
> skeleton in order to be able to compare each group.
>
> Cheers,
> Gwenaëlle
>
>
> --- En date de : Mar 21.4.09, Naama Barnea-Goraly
> <[log in to unmask]> a écrit :
>
>> De: Naama Barnea-Goraly <[log in to unmask]>
>> Objet: [FSL] Is this a valid thing to do? ( 3 groups tbss comparison)
>> À: [log in to unmask]
>> Date: Mardi 21 Avril 2009, 17h48
>> I have 3 groups: subjects, relatives and controls. We ran
>> separate t-tests to get our results, but now I would like to
>> show them on one image and when I overlay them they are
>> slightly "misregistered". I am assuming this is
>> because the registration is a little different in each
>> comparison. I would also like to extract the values from
>> regions of significant between group differences.
>>
>> Is it valid to run tbss_2- tbss_4 on all subjects (all 3
>> groups together) and then fslsplit/fslroi the groups that I
>> want, run analysis, generate images and extract values for
>> graphs?
>>
>> Thanks,
>>
>> Naama
>>
>>
>>
>> Naama Barnea-Goraly M.D.
>> Instructor
>> Center for Interdisciplinary Brain Sciences Research
>> Stanford University Division of Child and Adolescent
>> Psychiatry
>> 401 Quarry Rd. MC 5795
>> Stanford University School of Medicine
>> Stanford, CA 94305-5795
>> Phone: (650) 736-1874, fax: (650) 724-4794
>>
>>
>> CONFIDENTIALITY NOTICE: This e-mail communication and any
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>
>
>
Naama Barnea-Goraly M.D.
Instructor
Center for Interdisciplinary Brain Sciences Research
Stanford University Division of Child and Adolescent Psychiatry
401 Quarry Rd. MC 5795
Stanford University School of Medicine
Stanford, CA 94305-5795
Phone: (650) 736-1874, fax: (650) 724-4794
CONFIDENTIALITY NOTICE: This e-mail communication and any attachments
may contain confidential information for the use of the designated
recipients named above. If you are not the intended recipient, you
are hereby notified that you have received this communication in error
and that any review, disclosure, dissemination, distribution or
copying of it or its contents is prohibited. If you have received
this communication in error, please notify Stanford Medical Center
immediately by telephone at (650) 725-5722 and destroy all copies of
this communication and any attachments. Thank you.
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