subject:"\[Freesurfer\] FSFAST ROI atlas"

Re: [Freesurfer] FSFAST ROI atlas

2016-08-18 Thread Harms, Michael








Yes, the Gordon parcellation paper:

http://www.ncbi.nlm.nih.gov/pubmed/25316338





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sabin Khadka <mr.sabinkha...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, August 18, 2016 at 8:55 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael 
<mha...@wustl.edu> wrote:





They are attached (assuming that the FS list allows small attachments).
There is a script that details exactly how it was done.





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu






From: Sabin Khadka <mr.sabinkha...@gmail.com>
Date: Wednesday, August 17, 2016 at 11:25 AM
To: Freesurfer support list <freesur...@nmr.mgh.harvard.edu>, "Harms, Michael" <mha...@wustl.edu>


Subject: Re: [Freesurfer] FSFAST ROI atlas









Hi Michael- Is there anyway I can get those Gordon parcellation annot files?




Cheers,

Sabin Khadka




On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael 
<mha...@wustl.edu> wrote:






FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 
314-747-6173
St. Louis, MO  63110 Email: 
mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <gr...@nmr.mgh.harvard.edu>
Reply-To: "freesur...@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.edu>
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesur...@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:



Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!





Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
<gr...@nmr.mgh.harvard.edu> wrote:



I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:








HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 



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Re: [Freesurfer] FSFAST ROI atlas

2016-08-18 Thread Sabin Khadka

Hi Michael- Thanks very much for the file. Is there published paper or
other documents that I could use as reference for these annotation?

Cheers,
Sabin Khadka

On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael <mha...@wustl.edu> wrote:

>
> They are attached (assuming that the FS list allows small attachments).
> There is a script that details exactly how it was done.
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: Sabin Khadka <mr.sabinkha...@gmail.com>
> Date: Wednesday, August 17, 2016 at 11:25 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, "Harms,
> Michael" <mha...@wustl.edu>
>
> Subject: Re: [Freesurfer] FSFAST ROI atlas
>
> Hi Michael- Is there anyway I can get those Gordon parcellation annot
> files?
>
> Cheers,
> Sabin Khadka
>
> On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> FYI: I supplied a version of the “Gordon” parcellation in .annot format
>> to Bruce a while back.  He had expressed an interest in possibly including
>> it as part of FS 6.0.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <
>> gr...@nmr.mgh.harvard.edu>
>> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesur...@nmr.mgh.harvard.ed
>> u>
>> Date: Wednesday, August 17, 2016 at 9:55 AM
>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] FSFAST ROI atlas
>>
>> I don't know anything about the Power atlas. For the HCP, if they have it
>> in annotation format, then you can run mri_aparc2aseg to map it into the
>> anatomical volume, then specify that volume when you run fcseed-config. To
>> get the mri_aparc2aseg command line, look in the recon-all to find out how
>> aparc+aseg.mgz is created
>>
>> On 8/17/16 9:28 AM, Sabin Khadka wrote:
>>
>> Hi Doug- Do you think it is possible to use these atlas? If so could you
>> point me to steps that needed to be done.
>>
>> Thanks for your help!
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> I have not used them myself.
>>>
>>> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>>>
>>> HI all-
>>>
>>> I am using FSFAST to extract ROI time series values for further
>>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>>>
>>> However, I was wondering if anyone has used Power et.al 2011 rois
>>> and/or HCP's newly defined 180/per hemi rois to extract time series data.
>>> If so could you please advise me on how do it (if they are at all
>>> possible).
>>>
>>> Cheers,
>>> Sabin Khadka
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___ Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e
>>> du/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 error but does not contain patient information, please contact the
>>> sender and properly dispose of the e-mail.
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> --
>>
>> The mater

Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Sabin Khadka

Hi Michael- Is there anyway I can get those Gordon parcellation annot files?

Cheers,
Sabin Khadka

On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote:

>
> FYI: I supplied a version of the “Gordon” parcellation in .annot format to
> Bruce a while back.  He had expressed an interest in possibly including it
> as part of FS 6.0.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <
> gr...@nmr.mgh.harvard.edu>
> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu
> >
> Date: Wednesday, August 17, 2016 at 9:55 AM
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] FSFAST ROI atlas
>
> I don't know anything about the Power atlas. For the HCP, if they have it
> in annotation format, then you can run mri_aparc2aseg to map it into the
> anatomical volume, then specify that volume when you run fcseed-config. To
> get the mri_aparc2aseg command line, look in the recon-all to find out how
> aparc+aseg.mgz is created
>
> On 8/17/16 9:28 AM, Sabin Khadka wrote:
>
> Hi Doug- Do you think it is possible to use these atlas? If so could you
> point me to steps that needed to be done.
>
> Thanks for your help!
>
> Cheers,
> Sabin Khadka
>
> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu
> > wrote:
>
>> I have not used them myself.
>>
>> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>>
>> HI all-
>>
>> I am using FSFAST to extract ROI time series values for further
>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>>
>> However, I was wondering if anyone has used Power et.al 2011 rois and/or
>> HCP's newly defined 180/per hemi rois to extract time series data. If so
>> could you please advise me on how do it (if they are at all possible).
>>
>> Cheers,
>> Sabin Khadka
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___ Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e
>> du/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 error but does not contain patient information, please contact the
>> sender and properly dispose of the e-mail.
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> 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
> 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
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.

Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Harms, Michael








FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Doug Greve <gr...@nmr.mgh.harvard.edu>
Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:


Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!




Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
<gr...@nmr.mgh.harvard.edu> wrote:


I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:







HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___ 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 error but does not contain patient information, please contact the sender and properly dispose of the e-mail.





___
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


___
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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 error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Douglas Greve

I don't know anything about the Power atlas. For the HCP, if they have 
it in annotation format, then you can run mri_aparc2aseg to map it into 
the anatomical volume, then specify that volume when you run 
fcseed-config. To get the mri_aparc2aseg command line, look in the 
recon-all to find out how aparc+aseg.mgz is created



On 8/17/16 9:28 AM, Sabin Khadka wrote:
Hi Doug- Do you think it is possible to use these atlas? If so could 
you point me to steps that needed to be done.


Thanks for your help!

Cheers,
Sabin Khadka

On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
> wrote:


I have not used them myself.


On 8/15/16 10:23 AM, Sabin Khadka wrote:

HI all-

I am using FSFAST to extract ROI time series values for further
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.

However, I was wondering if anyone has used Power et.al
 2011 rois and/or HCP's newly defined 180/per hemi
rois to extract time series data. If so could you please advise
me on how do it (if they are at all possible).

Cheers,
Sabin Khadka


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___ Freesurfer mailing
list Freesurfer@nmr.mgh.harvard.edu

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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
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.

Re: [Freesurfer] FSFAST ROI atlas

2016-08-17 Thread Sabin Khadka

Hi Doug- Do you think it is possible to use these atlas? If so could you
point me to steps that needed to be done.

Thanks for your help!

Cheers,
Sabin Khadka

On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
wrote:

> I have not used them myself.
>
> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>
> HI all-
>
> I am using FSFAST to extract ROI time series values for further
> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>
> However, I was wondering if anyone has used Power et.al 2011 rois and/or
> HCP's newly defined 180/per hemi rois to extract time series data. If so
> could you please advise me on how do it (if they are at all possible).
>
> Cheers,
> Sabin Khadka
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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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] FSFAST ROI atlas

2016-08-15 Thread Douglas Greve


I have not used them myself.


On 8/15/16 10:23 AM, Sabin Khadka wrote:

HI all-

I am using FSFAST to extract ROI time series values for further 
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.


However, I was wondering if anyone has used Power et.al  
2011 rois and/or HCP's newly defined 180/per hemi rois to extract time 
series data. If so could you please advise me on how do it (if they 
are at all possible).


Cheers,
Sabin Khadka


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Freesurfer@nmr.mgh.harvard.edu
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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
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.

[Freesurfer] FSFAST ROI atlas

2016-08-15 Thread Sabin Khadka

HI all-

I am using FSFAST to extract ROI time series values for further
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.

However, I was wondering if anyone has used Power et.al 2011 rois and/or
HCP's newly defined 180/per hemi rois to extract time series data. If so
could you please advise me on how do it (if they are at all possible).

Cheers,
Sabin Khadka
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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
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.

Re: [Freesurfer] FSFAST ROI atlas

Re: [Freesurfer] FSFAST ROI atlas

Re: [Freesurfer] FSFAST ROI atlas

Re: [Freesurfer] FSFAST ROI atlas

Re: [Freesurfer] FSFAST ROI atlas

Re: [Freesurfer] FSFAST ROI atlas

Re: [Freesurfer] FSFAST ROI atlas

[Freesurfer] FSFAST ROI atlas

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