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
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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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___
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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+%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>
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<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields%C2%A0flags>?
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?
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65825.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,
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/msg65818.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>
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<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields%C2%A0flags>?
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?
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65814.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>
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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