Re: [Freesurfer] Regarding: Brainstem substructures
Hi Sampada, FS 6.0 is not out yet, but you can download the latest dev version from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ Using this version, you can run the brainstem module on subjects that have already been processed with 5.3. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Saturday, July 11, 2015 6:37:12 PM Subject: Re: [Freesurfer] Regarding: Brainstem substructures Thanks so much Bruce for your reply. when I open the link for brain stem structures ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ), it says This functionality is present in FreeSurfer 6.0 and later . And, when I go to the freesurfer download page, the only latest version of freesurfer (last updated by Zeke on 2015-06-02) I see is stable v5.3.0. If the version 6.0 is out, will you please send me the link so that I can download it? Thanks and regards, Sampada On Sat, Jul 11, 2015 at 7:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures ) but, I get the following error: ERROR: Flag -brainstem-structures unrecognized. -s IMRAN -brainstem-structures Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Will you please let me know where I am going wrong? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 version for my analysis. Thanks for your time! Kind regards, Sampada ___ 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
Re: [Freesurfer] Regarding: Brainstem substructures
Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) but, I get the following error: ERROR: Flag -brainstem-structures unrecognized. -s IMRAN -brainstem-structures Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Will you please let me know where I am going wrong? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 version for my analysis. Thanks for your time! Kind regards, Sampada ___ 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.
Re: [Freesurfer] Regarding: Brainstem substructures
Thanks so much Bruce for your reply. when I open the link for brain stem structures (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures), it says *This functionality is present in FreeSurfer https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer 6.0 and later* . And, when I go to the freesurfer download page, the only latest version of freesurfer (last updated by Zeke on 2015-06-02) I see is stable v5.3.0. If the version 6.0 is out, will you please send me the link so that I can download it? Thanks and regards, Sampada On Sat, Jul 11, 2015 at 7:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) but, I get the following error: ERROR: Flag -brainstem-structures unrecognized. -s IMRAN -brainstem-structures Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Will you please let me know where I am going wrong? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 version for my analysis. Thanks for your time! Kind regards, Sampada ___ 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] Regarding: Brainstem substructures
Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' ( https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) but, I get the following error: ERROR: Flag -brainstem-structures unrecognized. -s IMRAN -brainstem-structures Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Will you please let me know where I am going wrong? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 version for my analysis. Thanks for your time! Kind regards, Sampada ___ 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.
