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FSL  November 2010

FSL November 2010

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Subject:

Re: FSL FIRST different results on vertex analysis and volume analysis

From:

Bhavani shankara <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 23 Nov 2010 14:39:55 +0530

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (120 lines)

Dear Sir,

Thank you very much for all the information, it is very useful

On 11/23/10, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> Unfortunately we don't have any other correction method implemented
> currently, although we are working on them.  I cannot really comment on
> the biological implications of any of this, and caution you not to
> over-interpret
> anything as a non-significant result does *not* imply that there was nothing
> happening (or that it was intrinsically weaker) - it could be that, or it
> could just
> be that the specific noise you had manifest as differences in sensitivity
> that
> were like this, without any connection to biology.  This is especially true
> if
> one result is just over and another just under the statistical threshold.
> There
> is normally no interpretation that can be made from such a result.  If you
> are
> interested in laterality differences then you need to formulate a
> statistical
> test that directly looks for this and does not compare two different
> statistical
> results, as that is itself not a statistically valid approach.
>
> All the best,
> 	Mark
>
>
> On 22 Nov 2010, at 15:53, Bhavani shankara wrote:
>
>> Thanks for the reply,
>>
>> is their any other method through which i can try other correction method
>> (like FWE) to check the result. But on FDR uncorrected maps both
>> hippocampus are showing difference between the groups.
>>
>> Is it may be due to biological reason of differential involvement in the
>> structure of hippocampus between dominant and non-dominant hemispheres ??
>>
>> On Mon, Nov 22, 2010 at 9:16 PM, Mark Jenkinson <[log in to unmask]>
>> wrote:
>> Hi,
>>
>> This is perfectly reasonable for a couple of reasons:
>>
>>  1 - the volume change is not very spatially specific (or consistent)
>>        and hence you can have a strong overall volume change
>>        without a local vertex change (that is above threshold).
>>
>>  2 - the FDR thresholding is not the most sensitive technique for
>>        surface inference (we are working on coding up better ones)
>>        and so it is possible that it is just not quite sensitive enough
>>        although you might see interesting results in the uncorrected
>>        analyses.  Unfortunately, the FDR results are very dependent
>>        on the small p-values which can be significantly influenced by
>>        slight outliers.  It is worth looking at the uncorrected results to
>>        see if there is some consistent change which is just failing to
>>        meet the FDR threshold.
>>
>>
>> I hope this helps.
>> All the best,
>>        Mark
>>
>>
>>
>>
>>
>>
>> On 22 Nov 2010, at 04:58, Bhavani shankara wrote:
>>
>> > Dear FSL experts,
>> >
>> > I am using FSL-FIRST, on extracting the Volumes and statistics were done
>> > on R software and found the subcortical structures and also both left
>> > and right hippocampus were significantly differing between the groups
>> > (AD and controls (all are right handed) ) (p<0.01).
>> >
>> > However on vertex analysis only on left side hippocampus is not
>> > differing between the groups standing out at FDR correction (on using
>> > surface_fdr input.vtk). However other structures including the
>> > sub-cortical deep gray matter regions were differing at FDR threshold
>> > output (p value) below 0.05.
>> >
>> > Is it possible ?? is it due to technical/analysis issue or due to
>> > biological reason??
>> >
>> > Thanks in advance for your response
>> >
>> > --
>> > Dr. BHAVANI SHANKARA BAGEPALLY
>> > MBBS, (PhD in Clinical Neuroscience) NIMHANS,
>> > Bangalore,
>> > INDIA-560029
>> > email:  [log in to unmask]
>> >
>>
>>
>>
>> --
>> Dr. BHAVANI SHANKARA BAGEPALLY
>> MBBS, (PhD in Clinical Neuroscience) NIMHANS,
>> Bangalore,
>> INDIA-560029
>> email:  [log in to unmask]
>>
>


-- 
Dr. BHAVANI SHANKARA BAGEPALLY
MBBS, (PhD in Clinical Neuroscience) NIMHANS,
Bangalore,
INDIA-560029
email:  [log in to unmask]

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