Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-05-01 Thread Douglas N. Greve 

You have to turn it through autorecon3 (same as running with -all)
doug

On 5/1/2020 1:07 PM, Billah, Tashrif wrote:
Assuming `recon-all autorecon2 ...` requires completion of `recon-all 
autorecon1 ...` and autorecon3 requires completion of both 1 and 2, 
yes, I am asking which autorecon is sufficient.


-Tashrif

Are you asking whether you have to run recon-all all the way through 
inorder to run the subfields or whether one of the autorecons is 
sufficient?


On 5/1/2020 10:21 AM, Billah, Tashrif wrote:

 [Freesurfer] Which autorecon uses
 -hippocampal-subfields flags?
 
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html>


   2020-04-17
   
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread
   
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D++Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Billah,

   Tashrif
   
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>


   Douglas,

   Let's try with an example. See the two
   waysT2 image can be integrated with recon-all Altogether:
   recon-all -subject subjectname -i /path/to/input_volume -T2
   /path/to/T2_volume -T2pial -all autorecon3 only: recon-all
   -subject subjectname -T2 /path/to/T2_volume -T2pial
   -autorecon3 Similar to the former,
   -hippocampal-subfields-T1integrated with recon-all:
   recon-all -all -s bert -hippocampal-subfields-T1 Now the
   question, compared to the latter, which autorecon[1/2/3]
   would accept -hippocampal-subfields-T1? Does it make sense
   now? -Tashrif . ___ Freesurfer mailing list
   Freesurfer@nmr.mgh.harvard.edu
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


   Re: [Freesurfer] Which autorecon uses -hippocampal-subfields
   flags?
   
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html>



2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>DouglasN.

Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22&o=newest&f=1>


 I don't understand the question. To run recon-all through to the end
 implies that you have run all the -autorecons


 On 4/17/2020 2:53 PM, Billah, Tashrif wrote:

 Right, I understand the rule about the scripts.

 However, my original question was about the subfields
 -hippocampal-subfields-T1/T2/T1T2
 Again, can they be run with any of the autorecons separately? The
 example shown here
 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields>
 integrates the subfileds with recon-all only but do no show
 combination with any autorecon commands.


 -Tashrif
 .

 *From:* Billah, Tashrif
 *Sent:* Friday, April 17, 2020 1:52 PM
 *To:* freesurfer@nmr.mgh.harvard.edu
 *Subject:* Re: [Freesurfer] Which autorecon uses
 -hippocampal-subfields flags?

 Douglas,

 A little more elaboration would help. What is "it" and what are "them"?

 -Tashrif

 .



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   Re: [Freesurfer] Which autorecon uses -hippocampal-subfields
   flags?
   
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html>



2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Billah,Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>


 Right, I under

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-05-01 Thread Billah, Tashrif 
Assuming `recon-all autorecon2 ...` requires completion of `recon-all 
autorecon1 ...` and autorecon3 requires completion of both 1 and 2, yes, I am 
asking which autorecon is sufficient.

-Tashrif

Are you asking whether you have to run recon-all all the way through in order 
to run the subfields or whether one of the autorecons is sufficient?


On 5/1/2020 10:21 AM, Billah, Tashrif wrote:


[Freesurfer] Which autorecon uses
-hippocampal-subfields flags?

<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html>

  2020-04-17

<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread

<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D++Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Billah,
  Tashrif

<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>

  Douglas,

  Let's try with an example. See the two
  waysT2 image can be integrated with recon-all Altogether:
  recon-all -subject subjectname -i /path/to/input_volume -T2
  /path/to/T2_volume -T2pial -all autorecon3 only: recon-all
  -subject subjectname -T2 /path/to/T2_volume -T2pial
  -autorecon3 Similar to the former,
  -hippocampal-subfields-T1integrated with recon-all:
  recon-all -all -s bert -hippocampal-subfields-T1 Now the
  question, compared to the latter, which autorecon[1/2/3]
  would accept -hippocampal-subfields-T1? Does it make sense
  now? -Tashrif . ___ Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  Re: [Freesurfer] Which autorecon uses -hippocampal-subfields
  flags?

<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html>



2020-04-17 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread
 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Douglas
 N. Greve 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22&o=newest&f=1>

I don't understand the question. To run recon-all through to the end
implies that you have run all the -autorecons


On 4/17/2020 2:53 PM, Billah, Tashrif wrote:

Right, I understand the rule about the scripts.

However, my original question was about the subfields
-hippocampal-subfields-T1/T2/T1T2
Again, can they be run with any of the autorecons separately? The
example shown here
<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields>
integrates the subfileds with recon-all only but do no show
combination with any autorecon commands.


-Tashrif
    .

*From:* Billah, Tashrif
*Sent:* Friday, April 17, 2020 1:52 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Which autorecon uses
-hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?

-Tashrif

.



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  Re: [Freesurfer] Which autorecon uses -hippocampal-subfields
  flags?

<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html>



2020-04-17 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread
 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Billah,
 Tashrif 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>

Right, I understand the rule about the scripts.

However, my original question was about the subfields
-hippocampal-subfields-T1/T2/T1T2

Again, can they be run with any of the autorecons separately? The example
shown
here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields>
integrates
the subfileds with recon-all only but do no show combination with any
autorecon
commands.

-Tashrif
.

From: Billah, Tashrif
Sent: Friday, April 17, 2020 1:52 PM

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-05-01 Thread Douglas N. Greve 
Are you asking whether you have to run recon-all all the way through in 
order to run the subfields or whether one of the autorecons is sufficient?


On 5/1/2020 10:21 AM, Billah, Tashrif wrote:



[Freesurfer] Which autorecon uses
-hippocampal-subfields flags?

<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html>

  2020-04-17
  
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread
  
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D++Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Billah,
  Tashrif
  
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>

  Douglas,

  Let's try with an example. See the two
  waysT2 image can be integrated with recon-all Altogether:
  recon-all -subject subjectname -i /path/to/input_volume -T2
  /path/to/T2_volume -T2pial -all autorecon3 only: recon-all
  -subject subjectname -T2 /path/to/T2_volume -T2pial
  -autorecon3 Similar to the former,
  -hippocampal-subfields-T1integrated with recon-all:
  recon-all -all -s bert -hippocampal-subfields-T1 Now the
  question, compared to the latter, which autorecon[1/2/3]
  would accept -hippocampal-subfields-T1? Does it make sense
  now? -Tashrif . ___ Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


  Re: [Freesurfer] Which autorecon uses -hippocampal-subfields
  flags?
  
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html>

2020-04-17 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Douglas 
N. Greve 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22&o=newest&f=1>


I don't understand the question. To run recon-all through to the end
implies that you have run all the -autorecons


On 4/17/2020 2:53 PM, Billah, Tashrif wrote:

Right, I understand the rule about the scripts.

However, my original question was about the subfields
-hippocampal-subfields-T1/T2/T1T2
Again, can they be run with any of the autorecons separately? The
example shown here
<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields>
integrates the subfileds with recon-all only but do no show
combination with any autorecon commands.


-Tashrif
    .

*From:* Billah, Tashrif
*Sent:* Friday, April 17, 2020 1:52 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Which autorecon uses
-hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?

-Tashrif

.



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  Re: [Freesurfer] Which autorecon uses -hippocampal-subfields
  flags?
  
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html>

2020-04-17 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>Thread 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>Billah, 
Tashrif 
<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>


Right, I understand the rule about the scripts.

However, my original question was about the subfields
-hippocampal-subfields-T1/T2/T1T2

Again, can they be run with any of the autorecons separately? The example 
shown
here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 
integrates
the subfileds with recon-all only but do no show combination with any 
autorecon
commands.

-Tashrif
.

From: Billah, Tashrif
Sent: Friday, April 17, 2020 1:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas,

A little

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-05-01 Thread Billah, Tashrif 
[Freesurfer] Which autorecon uses -hippocampal-subfields 
flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html>
2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>
 
Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D++Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>
 Billah, 
Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>


Douglas,

Let's try with an example. See the two
ways T2 image can be
integrated with recon-all

Altogether:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume
-T2pial -all

autorecon3 only:

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

Similar to the former,
-hippocampal-subfields-T1
 integrated with recon-all:

recon-all -all -s bert -hippocampal-subfields-T1

Now the question, compared to the latter, which autorecon[1/2/3] would accept
-hippocampal-subfields-T1?

Does it make sense now?

-Tashrif
.
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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields 
flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html>
2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>
 
Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>
 Douglas N. 
Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22&o=newest&f=1>

I don't understand the question. To run recon-all through to the end
implies that you have run all the -autorecons


On 4/17/2020 2:53 PM, Billah, Tashrif wrote:

Right, I understand the rule about the scripts.

However, my original question was about the subfields
-hippocampal-subfields-T1/T2/T1T2
Again, can they be run with any of the autorecons separately? The
example shown here
<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields>
integrates the subfileds with recon-all only but do no show
combination with any autorecon commands.


-Tashrif
.

*From:* Billah, Tashrif
*Sent:* Friday, April 17, 2020 1:52 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Which autorecon uses
-hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?

-Tashrif

.



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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields 
flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html>
2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>
 
Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses+%5C-hippocampal%5C-subfields+flags%5C%3F%22&o=newest&f=1>
 Billah, 
Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=from:%22Billah%2C+Tashrif%22&o=newest&f=1>

Right, I understand the rule about the scripts.

However, my original question was about the subfields
-hippocampal-subfields-T1/T2/T1T2

Again, can they be run with any of the autorecons separately? The example shown
here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> integrates
the subfileds with recon-all only but do no show combination with any autorecon
commands.

-Tashrif
.

From: Billah, Tashrif
Sent: Friday, April 17, 2020 1:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?


-Tashrif

.

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields 
flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65827.html>
2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20200417&o=newest&f=1>
 
Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+Which+autorecon+uses

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-22 Thread Douglas N. Greve 

sorry, what question? Please include previous emails

On 4/21/2020 11:43 PM, Billah, Tashrif wrote:

Hello Douglas,

Waiting to hear back from you on my question

Thanks,
Tashrif

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-21 Thread Billah, Tashrif 
Hello Douglas,

Waiting to hear back from you on my question

Thanks,
Tashrif
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[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Billah, Tashrif 
Douglas,

Let's try with an example. See the two 
ways T2 image can be 
integrated with recon-all

Altogether:

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume 
-T2pial -all

autorecon3 only:

recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3

Similar to the former, 
-hippocampal-subfields-T1
 integrated with recon-all:

recon-all -all -s bert -hippocampal-subfields-T1

Now the question, compared to the latter, which autorecon[1/2/3] would accept 
-hippocampal-subfields-T1?

Does it make sense now?

-Tashrif
.
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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Douglas N. Greve 
I don't understand the question. To run recon-all through to the end 
implies that you have run all the -autorecons


On 4/17/2020 2:53 PM, Billah, Tashrif wrote:

Right, I understand the rule about the scripts.

However, my original question was about the subfields 
-hippocampal-subfields-T1/T2/T1T2
Again, can they be run with any of the autorecons separately? The 
example shown here 
<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> 
integrates the subfileds with recon-all only but do no show 
combination with any autorecon commands.


-Tashrif
.

*From:* Billah, Tashrif
*Sent:* Friday, April 17, 2020 1:52 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Which autorecon uses 
-hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?

-Tashrif

.



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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Billah, Tashrif 
Right, I understand the rule about the scripts.

However, my original question was about the subfields 
-hippocampal-subfields-T1/T2/T1T2

Again, can they be run with any of the autorecons separately? The example shown 
here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> integrates 
the subfileds with recon-all only but do no show combination with any autorecon 
commands.

-Tashrif
.

From: Billah, Tashrif
Sent: Friday, April 17, 2020 1:52 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

Douglas,

A little more elaboration would help. What is "it" and what are "them"?


-Tashrif

.

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Douglas N. Greve 
You have to run recon-all all the way through and then run the subfield 
scripts separately.


On 4/17/2020 12:21 PM, Douglas N. Greve wrote:
None! You have to run it all the way through to the end and then run 
them from the command line.


On 4/17/2020 11:40 AM, Billah, Tashrif wrote:

Hi all,

Which of the three autorecons makes use of 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags?

autorecon1, 2 , or 3?

My goal is to use the flag specifically with one of the three and not 
with recon-all in general as shown in the above page.


I do understand that the new version of the commands are 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


Best,
Tashrif


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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Billah, Tashrif 
Douglas,

A little more elaboration would help. What is "it" and what are "them"?


-Tashrif

.

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Douglas N. Greve 
None! You have to run it all the way through to the end and then run 
them from the command line.


On 4/17/2020 11:40 AM, Billah, Tashrif wrote:

Hi all,

Which of the three autorecons makes use of 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags?

autorecon1, 2 , or 3?

My goal is to use the flag specifically with one of the three and not 
with recon-all in general as shown in the above page.


I do understand that the new version of the commands are 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala


Best,
Tashrif


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[Freesurfer] Which autorecon uses -hippocampal-subfields flags?

2020-04-17 Thread Billah, Tashrif 
Hi all,

Which of the three autorecons makes use of 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags?
autorecon1, 2 , or 3?

My goal is to use the flag specifically with one of the three and not with 
recon-all in general as shown in the above page.

I do understand that the new version of the commands are 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

Best,
Tashrif

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