External Email - Use Caution
Hello FreeSufer developers,
We're trying to have a small quality control pipeline when executing recon-all. As a part of this, one doubt came to us, and couldn't find an answer:
Is the -cw256 flag applied always or only when the FOV is larger than expected? Also, when executing -autorecon1 and -autorecon2 separately, should we use this flag only in -autorecon1 or also in -autorecon2 and -autorecon3? I tried applying only to -autorecon1 and it worked apparently, but I don't know if I'm missing something.
We're using the following version of Freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I would be more than grateful for any help, and sorry if that might be a lame question.
Sincerely,
Javier Rojo Muñoz
It will always apply it. If your data are 256 anyway, it will not have an effect. If your data are <256, then it will have some small effects
On 05/03/2018 04:30 AM, JAVIER ROJO MUÑOZ wrote:
External Email - Use CautionHello FreeSufer developers,
We're trying to have a small quality control pipeline when executing recon-all. As a part of this, one doubt came to us, and couldn't find an answer:
Is the -cw256 flag applied always or only when the FOV is larger than expected? Also, when executing -autorecon1 and -autorecon2 separately, should we use this flag only in -autorecon1 or also in -autorecon2 and -autorecon3? I tried applying only to -autorecon1 and it worked apparently, but I don't know if I'm missing something.
We're using the following version of Freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I would be more than grateful for any help, and sorry if that might be a lame question.
Sincerely,
Javier Rojo Muñoz
External Email - Use Caution
El 2018-05-07 19:54, Douglas N. Greve escribió:
It will always apply it. If your data are 256 anyway, it will not have an effect. If your data are <256, then it will have some small effects
On 05/03/2018 04:30 AM, JAVIER ROJO MUÑOZ wrote:
External Email - Use CautionHello FreeSufer developers,
We're trying to have a small quality control pipeline when executing recon-all. As a part of this, one doubt came to us, and couldn't find an answer:
Is the -cw256 flag applied always or only when the FOV is larger than expected? Also, when executing -autorecon1 and -autorecon2 separately, should we use this flag only in -autorecon1 or also in -autorecon2 and -autorecon3? I tried applying only to -autorecon1 and it worked apparently, but I don't know if I'm missing something.
We're using the following version of Freesurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I would be more than grateful for any help, and sorry if that might be a lame question.
Sincerely,
Javier Rojo Muñoz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you really much for the help! About the second part of the question, indeed I've reread the wiki and I must have missed the explanation about the <subj>/tmp/cw256 folder last time. Sorry for that error of me, and thank you again.
Sincerely
Javier Rojo Muñoz
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
JAVIER ROJO MUÑOZ