Re: [Freesurfer] FreeSurfer atlas and statistics question

[Huang, Yujing]

Hi Jacob,

I hope this page will provide some information you are looking for - 
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

BA/BA.thresh stats are computed with annotations created from a set of labels 
included in Freesurfer.

I think by default Freesurfer uses ?h.aparc.annot (Desikan-Killiany cortical 
atlas) to compute the stats.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Levman, Jacob
Sent: Friday, January 20, 2023 9:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer atlas and statistics question

To whom it may concern among FreeSurfer staff,

My colleagues and I have performed an analysis with FreeSurfer that is under 
peer review. The reviewer has asked that we detail each atlas relied upon and 
connect that with each of the statistics that we relied upon in our analysis.

The statistics that we relied upon were the .stats data from each of the 
following: aparc, aparc.DKTatlas40, aparc.a2009s, BA, BA.thresh, w-g.pct, curv, 
entorhinal_exvivo, wmparc, aseg.

Obviously we use the Desikan-Killiany-Tourville atlas (and aparc.DKTatlas40 
statistics were extracted from that atlas).
I know there are other atlases, such as the Destrieux atlas, etc., but I'm not 
certain which of the above codes were extracted from Destrieux, and which ones 
were extracted from other atlases (and the names of those other atlases).

We ran a recon-all command for this study, but we only used the statistics 
outlined above (aparc, aparc.DKTatlas40, etc.). We need a list of all atlases 
supported with recon-all, and which ones were relied upon to generate each of 
the statistics codes in the above list.

Perhaps there is a complete list on a website somewhere of all the atlases and 
which of these .stats codes came from which atlas, but my searches online have 
not revealed the appropriate website. Could someone answer this question, or 
direct me to a complete website with all these details?

Thanks so much for your assistance!

Jacob
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Re: [Freesurfer] FreeSurfer Atlas

[Bruce Fischl]

you can always look in the recon-all script - the atlas (*.gca) file we 
use is listed in there.


cheers
Bruce
On Thu, 13 Oct 2016, GAJENDRA KATUWAL (RIT Student) 
wrote:



According to this website
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3, Freesurfer v
3.0 uses Aseg atlas for the segmentation of subcortical structures.
It does not explicitly mention anything about Freesurfer v5.3 though. 

On Thu, Oct 13, 2016 at 8:02 AM, AKUDJEDU, THEOPHILUS
 wrote:


  Hi All,


  Which default atlas does FreeSurfer 5.3 use for the segmentation
  of subcortical structures?


  Thanks


  Theo



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Re: [Freesurfer] FreeSurfer Atlas

[GAJENDRA KATUWAL (RIT Student)]

According to this website
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3, Freesurfer v
3.0 uses Aseg atlas for the segmentation of subcortical structures.
It does not explicitly mention anything about Freesurfer v5.3 though.

On Thu, Oct 13, 2016 at 8:02 AM, AKUDJEDU, THEOPHILUS <
t.akudje...@nuigalway.ie> wrote:

>
> Hi All,
>
>
> Which default atlas does FreeSurfer 5.3 use for the segmentation of
> subcortical structures?
>
>
> Thanks
>
>
> Theo
>
>
> ___
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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
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> HelpLine at
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> 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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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


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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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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 and template

[Bruce Fischl]

Hi Guang,

there are a number of atlases in FreeSurfer and some of them contain 
disease populations (Alzheimer's). As for 3T, we might do this, although we 
prefer to focus our efforts on making the tools insensitive to field 
strength.

cheers
Bruce



On Wed, 10 
Mar 2010, Guang Zeng wrote:

>
> Hello, there,
>
> I have two questions about FreeSurfer default atlas and template,
>
> Will Freesurfer team build an atlas or template using 3T scans in future?
>
> Will Freesurfer team build an atlas or template using patients with disease 
> in future?
>
> Thanks!
> Guang
>
> _
> Hotmail: Free, trusted and rich email service.
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