Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it?
On Jun 25, 2015, at 13:36, Allison Moreau almoreau@nmr.mgh.harvard.edu wrote:
Hi Falk and Thomas,
We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6.
-Allison
On 06/25/2015 07:09 AM, Falk Lüsebrink wrote:
Hi Thomas,
this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data.
Best, Falk
P.S. Following your instructions one will definitely become a coffee junkie. :D
Von: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
Hello!
I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments!
Best, Thomas
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High resolution fMRI has always been supported. V6 beta has better support for high-resolution structurals. If your fMRI is higher than 1mm isotropic then having higher res structurals (and hence denser cortical meshes) might be useful
cheers Bruce
On Sat, 17 Oct 2015, Yun Wang wrote:
Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it?
On Jun 25, 2015, at 13:36, Allison Moreau <almoreau@nmr.mgh.harvard.edu> wrote:Hi Falk and Thomas,
We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6.
-Allison
On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas, this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data. Best, Falk P.S. Following your instructions one will definitely become a coffee junkie. :D Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data Hello! I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments! Best, Thomas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline%C2%A0. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Glad to hear this ! So how should I specify high resolution structure using recon-all command?
On Oct 17, 2015, at 10:09, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
High resolution fMRI has always been supported. V6 beta has better support for high-resolution structurals. If your fMRI is higher than 1mm isotropic then having higher res structurals (and hence denser cortical meshes) might be useful
cheers Bruce
On Sat, 17 Oct 2015, Yun Wang wrote:
Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it?
On Jun 25, 2015, at 13:36, Allison Moreau <almoreau@nmr.mgh.harvard.edu> wrote:Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas,
this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data.
Best, Falk
P.S. Following your instructions one will definitely become a coffee junkie. :D
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
Hello!
I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments!
Best, Thomas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you can use the -cm flag, but you might want to try out a beta of v6 instead of 5.3 On Sun, 18 Oct 2015, Yun Wang wrote:
Glad to hear this ! So how should I specify high resolution structure using recon-all command?
On Oct 17, 2015, at 10:09, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
High resolution fMRI has always been supported. V6 beta has better support for high-resolution structurals. If your fMRI is higher than 1mm isotropic then having higher res structurals (and hence denser cortical meshes) might be useful
cheers Bruce
On Sat, 17 Oct 2015, Yun Wang wrote:
Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it?
On Jun 25, 2015, at 13:36, Allison Moreau <almoreau@nmr.mgh.harvard.edu> wrote:Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas,
this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data.
Best, Falk
P.S. Following your instructions one will definitely become a coffee junkie. :D
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
Hello!
I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments!
Best, Thomas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It works pretty well, thanks !
On Oct 18, 2015, at 14:10, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you can use the -cm flag, but you might want to try out a beta of v6 instead of 5.3 On Sun, 18 Oct 2015, Yun Wang wrote:
Glad to hear this ! So how should I specify high resolution structure using recon-all command?
On Oct 17, 2015, at 10:09, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
High resolution fMRI has always been supported. V6 beta has better support for high-resolution structurals. If your fMRI is higher than 1mm isotropic then having higher res structurals (and hence denser cortical meshes) might be useful
cheers Bruce
On Sat, 17 Oct 2015, Yun Wang wrote:
Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it?
On Jun 25, 2015, at 13:36, Allison Moreau <almoreau@nmr.mgh.harvard.edu> wrote:Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas,
this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data.
Best, Falk
P.S. Following your instructions one will definitely become a coffee junkie. :D
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
Hello!
I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments!
Best, Thomas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi,
I recently using Freesurfer 6 beta version to recon high resolution data with the -cm flag, however, the program exit with error. total defect index = 0
\n mris_euler_number ../surf/rh.orig \n
Darwin AlbertStekiiMac 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
recon-all -s HIP001_3d exited with ERRORS at Thu Oct 22 08:15:53 CDT 2015
Attached is the whole log history.
Thanks for any idea!
Yun
On Oct 18, 2015, at 14:10, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you can use the -cm flag, but you might want to try out a beta of v6 instead of 5.3 On Sun, 18 Oct 2015, Yun Wang wrote:
Glad to hear this ! So how should I specify high resolution structure using recon-all command?
On Oct 17, 2015, at 10:09, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
High resolution fMRI has always been supported. V6 beta has better support for high-resolution structurals. If your fMRI is higher than 1mm isotropic then having higher res structurals (and hence denser cortical meshes) might be useful
cheers Bruce
On Sat, 17 Oct 2015, Yun Wang wrote:
Can the recon-all for high resolution fMRI data be used in V6 beta freesurfer now? If so, how to use it?
On Jun 25, 2015, at 13:36, Allison Moreau <almoreau@nmr.mgh.harvard.edu> wrote:Hi Falk and Thomas, We are actually working on testing the -hires flag now for the v6 release. We intend to release it with v6. -Allison On 06/25/2015 07:09 AM, Falk Lüsebrink wrote: Hi Thomas,
this looks like a really nice script and a lot better than my own. In the upcoming release of FreeSurfer v.6 my work-around probably is not needed anymore. However, I haven’t been able to have a look at the dev release yet and whether the standard recon-all features a flag to process high resolution data.
Best, Falk
P.S. Following your instructions one will definitely become a coffee junkie. :D
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard .edu] Im Auftrag von Emmerling Thomas (PSYCHOLOGY) Gesendet: Mittwoch, 24. Juni 2015 14:35 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] recon-all pipeline for (sub-millimeter) 7T data
Hello!
I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments!
Best, Thomas _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Yun Wang