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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[Freesurfer] FreeSurfer atlas and statistics question

[Levman, Jacob]

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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 .
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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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] FreeSurfer Atlas

[AKUDJEDU, THEOPHILUS]

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 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
lzol...@nmr.mgh.harvard.eduwrote:


 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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 is
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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline.
  If the e-mail was sent to you in error
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 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 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


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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
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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
lzol...@nmr.mgh.harvard.eduwrote:


 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/**compliancelinehttp://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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[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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[Freesurfer] freesurfer atlas and template

[Guang Zeng]

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
  
_
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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.
 http://clk.atdmt.com/GBL/go/201469228/direct/01/
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