[Freesurfer] [FREESURFER] atlas applicability.

[Cheol Han]

Hello freesurfers


I am using freesurfer for patients with various neural disease. I wonder
the the freesurfer atlas is applicable to them: dementia (with Lewy bodies,
DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some
studies already used freesurfer for some of the diseases in the list,) I
believe epilepsy patients with lobectomy cannot be applicable.

Also is there age limit for the freesurfer atlas? How young can the atlas
work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the
upper bound? 80 year-old?

Thanks for reading and your time!


Best
Cheol





Cheol Han, Ph.D
Computational Neuroscience and Neuroinformatics
Department of Brain and Cognitive Sciences
Seoul National University
Korea
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Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)

[Lilla Zollei]

Hi Cheol,

I am using freesurfer for patients with various neural disease. I wonder the 
the

freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB),
epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies 
already

used freesurfer for some of the diseases in the list,) I believe epilepsy
patients with lobectomy cannot be applicable.  


If the malformation or the difference between normal control acquisitions 
and your scans is significant the FS pipeline, using the FS atlas is not 
going to be successful. Withuot seeing your data I cannot tell which 
population from the above is going to be affected, but if in doubt just 
try processing one or two representative samples from the different 
populations and assess how successful the processing is.


Also is there age limit for the freesurfer atlas? How young can the atlas 
work

for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper
bound? 80 year-old? 


The lower bound, in our experience, is about 4-5 yrs. Of course, it 
depends on your data quality but we had success all the way down to that 
age. I am not aware of any upper limits. Again, if you are processing 
these kind of "extreme" populations, make sure that you inspect the 
outcome of the FS recon pipeline carefully before proceeding with any 
type of analysis.


Lilla___
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Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)

[Cheol Han]

Dear Lilla

I appreciate your answers. It was very helpful. Just another follow-up
question. I think freesurfer itself ended without errors and the
skull-stripped and surfaces look okay. I think in the recommended
reconstruction Pipeline, "check segmentation" is related to checking atlas
worked. Still, I wonder there is a gold standard to check the atlas
(Deksian atlas) works okay. .

Thanks again!

Best
Cheol


Cheol Han, Ph.D
Computational Neuroscience and Neuroinformatics
Department of Brain and Cognitive Sciences
Seoul National University
Korea


On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei
wrote:

>
> Hi Cheol,
>
>
>  I am using freesurfer for patients with various neural disease. I wonder
>> the the
>> freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB),
>> epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies
>> already
>> used freesurfer for some of the diseases in the list,) I believe epilepsy
>> patients with lobectomy cannot be applicable.
>>
>
> If the malformation or the difference between normal control acquisitions
> and your scans is significant the FS pipeline, using the FS atlas is not
> going to be successful. Withuot seeing your data I cannot tell which
> population from the above is going to be affected, but if in doubt just try
> processing one or two representative samples from the different populations
> and assess how successful the processing is.
>
>
>  Also is there age limit for the freesurfer atlas? How young can the atlas
>> work
>> for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper
>> bound? 80 year-old?
>>
>
> The lower bound, in our experience, is about 4-5 yrs. Of course, it
> depends on your data quality but we had success all the way down to that
> age. I am not aware of any upper limits. Again, if you are processing these
> kind of "extreme" populations, make sure that you inspect the outcome of
> the FS recon pipeline carefully before proceeding with any type of analysis.
>
> Lilla
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)

[Lilla Zollei]

Hi Cheol,

I am a bit confused by your question. The atlases that we use help with 
the segmentation on the surface reconstruction steps when we process a new 
volume. If the outcomes look resonable to you, then all is good. Did I 
answer your question?


Lilla

On Fri, 30 Mar 2012, Cheol Han wrote:


Dear Lilla 
I appreciate your answers. It was very helpful. Just another follow-up question. I think 
freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I 
think in the recommended reconstruction Pipeline, "check segmentation" is 
related to
checking atlas worked. Still, I wonder there is a gold standard to check the 
atlas (Deksian atlas) works okay. .

Thanks again!

Best
Cheol


Cheol Han, Ph.D
Computational Neuroscience and Neuroinformatics
Department of Brain and Cognitive Sciences
Seoul National University
Korea


On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei  
wrote:

  Hi Cheol,

I am using freesurfer for patients with various neural disease. I 
wonder the the
freesurfer atlas is applicable to them: dementia (with Lewy bodies, 
DLB),
epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some 
studies already
used freesurfer for some of the diseases in the list,) I believe 
epilepsy
patients with lobectomy cannot be applicable.  


If the malformation or the difference between normal control acquisitions and 
your scans is significant the FS pipeline, using the FS atlas is not going to 
be successful. Withuot seeing your data I cannot tell which population from the 
above is going to be
affected, but if in doubt just try processing one or two representative samples 
from the different populations and assess how successful the processing is.

  Also is there age limit for the freesurfer atlas? How young can the atlas 
work
  for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper
  bound? 80 year-old? 


The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data 
quality but we had success all the way down to that age. I am not aware of any upper 
limits. Again, if you are processing these kind of "extreme" populations, make 
sure
that you inspect the outcome of the FS recon pipeline carefully before 
proceeding with any type of analysis.

Lilla


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)

[Cheol Han]

Dear Lilla

Yes, It is clear now!

Best
Cheol



Cheol Han, Ph.D
Computational Neuroscience and Neuroinformatics
Department of Brain and Cognitive Sciences
Seoul National University
Korea


On Fri, Mar 30, 2012 at 8:40 AM, Lilla Zollei
wrote:

>
> Hi Cheol,
>
> I am a bit confused by your question. The atlases that we use help with
> the segmentation on the surface rec



> onstruction steps when we process a new volume. If the outcomes look
> resonable to you, then all is good. Did I answer your question?
>
> Lilla
>
>
> On Fri, 30 Mar 2012, Cheol Han wrote:
>
>  Dear Lilla
>> I appreciate your answers. It was very helpful. Just another follow-up
>> question. I think freesurfer itself ended without errors and the
>> skull-stripped and surfaces look okay. I think in the recommended
>> reconstruction Pipeline, "check segmentation" is related to
>> checking atlas worked. Still, I wonder there is a gold standard to check
>> the atlas (Deksian atlas) works okay. .
>>
>> Thanks again!
>>
>> Best
>> Cheol
>>
>>
>> Cheol Han, Ph.D
>> Computational Neuroscience and Neuroinformatics
>> Department of Brain and Cognitive Sciences
>> Seoul National University
>> Korea
>>
>>
>> On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei <
>> lzol...@nmr.mgh.harvard.edu> wrote:
>>
>>  Hi Cheol,
>>
>>I am using freesurfer for patients with various neural
>> disease. I wonder the the
>>freesurfer atlas is applicable to them: dementia (with Lewy
>> bodies, DLB),
>>epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some
>> studies already
>>used freesurfer for some of the diseases in the list,) I
>> believe epilepsy
>>patients with lobectomy cannot be applicable.
>>
>>
>> If the malformation or the difference between normal control acquisitions
>> and your scans is significant the FS pipeline, using the FS atlas is not
>> going to be successful. Withuot seeing your data I cannot tell which
>> population from the above is going to be
>> affected, but if in doubt just try processing one or two representative
>> samples from the different populations and assess how successful the
>> processing is.
>>
>>  Also is there age limit for the freesurfer atlas? How young can the
>> atlas work
>>  for? 4 year-old? 6 year-old? or more than 10 year-old? How about the
>> upper
>>  bound? 80 year-old?
>>
>>
>> The lower bound, in our experience, is about 4-5 yrs. Of course, it
>> depends on your data quality but we had success all the way down to that
>> age. I am not aware of any upper limits. Again, if you are processing these
>> kind of "extreme" populations, make sure
>> that you inspect the outcome of the FS recon pipeline carefully before
>> proceeding with any type of analysis.
>>
>> Lilla
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.