[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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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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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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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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Douglas,

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

-Tashrif

.

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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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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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