Follow up on this question - upon careful inspection it seems that the
results of the individual t-tests run on two group registration and
results of the t-tests run on the 3 group registration are a little
different.
Essentially the clusters are slightly less significant in the (2
group) t-tests done with the skeleton derived from the 3 group
registration such that if Iook at the results at 0.05 in the 3 groups
they will look the same as at 0.01 at the 2 groups registration. If I
increase the threshold to 0.01 at the 3 group registration some
smaller clusters will be lost. So my question is which results are
valid and should be reported?
Thanks,
Naama
On Apr 21, 2009, at 9:51 AM, Gwenaëlle DOUAUD wrote:
> Hi Naama,
>
> yes you're right, in this case, this is better to run tbss3 with the
> -S option...
>
> 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: Re: [FSL] Re : [FSL] Is this a valid thing to do? ( 3 groups
>> tbss comparison)
>> À: [log in to unmask]
>> Date: Mardi 21 Avril 2009, 18h36
>> 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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>> 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.
>>>
>>>
>>>
>>
>> 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.
>
>
>
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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