parallel recon-all using T1,T2 images

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Toshiharu Kamishikiryo

27 Apr 2023 27 Apr '23

3:15 a.m.

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Hello Freesurfer experts

I am trying to recon-all using T2 images as well to improve pial surfaces. Does anyone know how to use GNU Parallel in bash to run the following commands in parallel?

recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii -T2pial -all -qcache

Thanks in advance.

Regards Kamishikiryo Research Student

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Michael Mc Laughlin

27 Apr 27 Apr

5:45 a.m.

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That is a single command. How can you run a single command in parallel?

You can add the -parallel flag to get freesurfer to run recon-all in parallel threads.

On Thu, Apr 27, 2023 at 8:16 AM Toshiharu Kamishikiryo k5105880@gmail.com wrote:

...

    External Email - Use Caution
Hello Freesurfer experts

I am trying to recon-all using T2 images as well to improve pial surfaces. Does anyone know how to use GNU Parallel in bash to run the following commands in parallel?

recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii -T2pial -all -qcache

Thanks in advance.

Regards Kamishikiryo Research Student

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/11IT50yO70no-TpnGGtxNBPxXIXcNelFSs1XUyTzCMlINgt... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1UVq-6A-KZL6nh8tp5FGqIx7fwuFzn0U1COgFIAP218fs4k... < https://secure-web.cisco.com/1UVq-6A-KZL6nh8tp5FGqIx7fwuFzn0U1COgFIAP218fs4k... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

Douglas N. Greve

28 Apr 28 Apr

10:32 a.m.

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I'm not sure the parallel flag works any more. But you can specify multiple threads with -threads N

On 4/27/2023 5:45 AM, Michael Mc Laughlin wrote:

...

External Email - Use Caution

That is a single command. How can you run a single command in parallel?

You can add the -parallel flag to get freesurfer to run recon-all in parallel threads.

On Thu, Apr 27, 2023 at 8:16 AM Toshiharu Kamishikiryo k5105880@gmail.com wrote:

        External Email - Use Caution

Hello Freesurfer experts

I am trying to recon-all using T2 images as well to improve pial
surfaces. Does anyone know how to use GNU Parallel in bash to run
the following commands in parallel?

recon-all -subject subjectname -i /path/to/T1w.nii -T2
/path/to/T2w.nii -T2pial -all -qcache

Thanks in advance.

Regards
Kamishikiryo
Research Student


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Toshiharu Kamishikiryo

27 Apr 27 Apr

9:42 a.m.

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Thanks for pointing that out, sir.

2023年4月27日(木) 16:15 Toshiharu Kamishikiryo k5105880@gmail.com:

...

Hello Freesurfer experts

I am trying to recon-all using T2 images as well to improve pial surfaces. Does anyone know how to use GNU Parallel in bash to run the following commands in parallel?

recon-all -subject subjectname -i /path/to/T1w.nii -T2 /path/to/T2w.nii -T2pial -all -qcache

Thanks in advance.

Regards Kamishikiryo Research Student

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Douglas N. Greve
Michael Mc Laughlin
Toshiharu Kamishikiryo