parallel recon-all using T1,T2 images

List overview All Threads
Download

newer

older

substantia nigra

Any large stash of labelled brain...

Toshiharu Kamishikiryo

27 Apr 2023 27 Apr '23

3:15 a.m.

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

Attachments:

attachment.html (text/html — 977 bytes)

Show replies by date

Michael Mc Laughlin

27 Apr 27 Apr

5:45 a.m.

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

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.

External Email - Use Caution

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


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://secure-web.cisco.com/1c4roIn8nLPk6CdvSrC3ssvxG7CAEIrvZ9XVy-h9nzyyfXQOeZgGwtBksXDrXzmO2VmJiW2TBRC58UR1nsfR1zxSsS33EQBOX82vD0UWzP5Lt24jJpQZZGBCTmPtnMmr5CIUE666ZgX99gIpqJRdo8oZP-ccpNNml1H_KJCPDLHdcAkAybZCxHbfAiJTzQ8ZEBjFwxkUGzXq0oWSF9oSeTAFGjslw91bGf27OQ8XPdQvQDuN2vpXsag1_42NyXIqRd5iUfjLurWmSH-EZPIMpQQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
<https://secure-web.cisco.com/11IT50yO70no-TpnGGtxNBPxXIXcNelFSs1XUyTzCMlINgtr3sm7O4WYroRES8v0eQiZH3S8BMK4V0GFti69voxlr-pzH2RjfZnWEeEFBghYdIZ-r0GKYSyDgLLPqf1zkbGW-ndykWIROAvpLRJad81sWkdJx-cd6Gud0iEK7f9yc0m0uglVE3TY_MwVqoVyM2jvYqgSIUeWddNAslePwHdnULqGCwE2BdyWwUt6M9o8jc9WYODKWV_fOqZWGSMd9GwHe3xUGfMBkiczHjn-Lqw1oeHF3aB_xIVbA5Fizn-H4R-0ct-ElhJ2uvizbaq9m/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://secure-web.cisco.com/1_2t172UnFJP9j6E_QZkBJIZIc2afKz412wPWVCXqB1Hj-qx7fIVofEnylk1h6rrncfLSqdePa30jNWRst7eDxRrGJyBw_IkCoZ9HSFTmrc81qs4iUr9GOITL9DWI822yul3w2_IuORXJxMGpyh3bGR4JwMwnPz3UgJOxO0ZwGOO0iyN7SRiLWVCHPrOFaNXoblIXJWPuiN6OqRe_lIRqfb22hki8uiNOLBQxpJtu8xFpbM0KzF1AOa50dYIdMhWbHE_l63CtJ5wHBQ4ekS0PXQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
<https://secure-web.cisco.com/1UVq-6A-KZL6nh8tp5FGqIx7fwuFzn0U1COgFIAP218fs4ko9LCuCYiazA0ixFn1WcGO0DmU4Lzc5U8IuaUWeWLMeY6A-SovdoXO8fjJ7yd2umlhMavZVwimFJh9_v_GYQdxiX4dq2kPJ-GAHw0NnFgzinfAeyPccMGEI6JAVI60_gLg5kJiQc1B4h21om0fayuGgk09F8EEWmPwb2-7xqRFbM8PRgyHV7ln53nXrKhhZyT5a3_En7xhjdSQboQK9hCzzSeu3clmv_GPereBSRiQa0gSV7TQvPK64I-MLSUg81y-WVR4NZehnOJJFd-o4/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
<*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://secure-web.cisco.com/1_2t172UnFJP9j6E_QZkBJIZIc2afKz412wPWVCXqB1Hj-qx7fIVofEnylk1h6rrncfLSqdePa30jNWRst7eDxRrGJyBw_IkCoZ9HSFTmrc81qs4iUr9GOITL9DWI822yul3w2_IuORXJxMGpyh3bGR4JwMwnPz3UgJOxO0ZwGOO0iyN7SRiLWVCHPrOFaNXoblIXJWPuiN6OqRe_lIRqfb22hki8uiNOLBQxpJtu8xFpbM0KzF1AOa50dYIdMhWbHE_l63CtJ5wHBQ4ekS0PXQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
<https://secure-web.cisco.com/1UVq-6A-KZL6nh8tp5FGqIx7fwuFzn0U1COgFIAP218fs4ko9LCuCYiazA0ixFn1WcGO0DmU4Lzc5U8IuaUWeWLMeY6A-SovdoXO8fjJ7yd2umlhMavZVwimFJh9_v_GYQdxiX4dq2kPJ-GAHw0NnFgzinfAeyPccMGEI6JAVI60_gLg5kJiQc1B4h21om0fayuGgk09F8EEWmPwb2-7xqRFbM8PRgyHV7ln53nXrKhhZyT5a3_En7xhjdSQboQK9hCzzSeu3clmv_GPereBSRiQa0gSV7TQvPK64I-MLSUg81y-WVR4NZehnOJJFd-o4/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
.
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.

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1c4roIn8nLPk6CdvSrC3ssvxG7CAEIrvZ9XVy-h9nzyyfXQ...

Toshiharu Kamishikiryo

27 Apr 27 Apr

9:42 a.m.

External Email - Use Caution

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

1203

Age (days ago)

1204

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

3 comments

3 participants

tags (0)

participants (3)

Douglas N. Greve
Michael Mc Laughlin
Toshiharu Kamishikiryo