I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the difference between this and the apart.annot is? Does it just have 40 labels versus the 36 found in the older version?
Thanks!
You can read about it here: http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00171/ab... ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of krista kelly [krista.kelly16@gmail.com] Sent: Saturday, November 16, 2013 8:01 PM To: freesurfer Subject: [Freesurfer] aparc.DKTatlas40
I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the difference between this and the apart.annot is? Does it just have 40 labels versus the 36 found in the older version?
Thanks!
Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues.Thank you very much for your attention,Pablo
Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues.Thank you very much for your attention,Pablo
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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 Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. *PloS one*, *7*(6), e38234. doi:10.1371/journal.pone.0038234).
for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari
On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablonajt@hotmail.com wrote:
Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel).
I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo
_______________________________________________ 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.
Dear Gari,Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6?Thanks,Pablo
From: garikoitz@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Hi Pablo,you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. PloS one, 7(6), e38234. doi:10.1371/journal.pone.0038234).
for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too).regards!Gari
On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablonajt@hotmail.com wrote:
Dear FS experts,I am forwarding my question (please see below), in case it got lost among the intense flow of messages.Thank you for your consideration.Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 +0000
Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts,I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel).
I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream.
Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues.
Thank you very much for your attention,Pablo
_______________________________________________ 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
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.
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablonajt@hotmail.com wrote:
Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo
From: garikoitz@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. *PloS one*, *7*(6), e38234. doi:10.1371/journal.pone.0038234).
for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari
On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablonajt@hotmail.com wrote:
Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel).
I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo
_______________________________________________ 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 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.
I have to agree with Gari, I see no reason for you to not use the CentOS6 build.
-Zeke
On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote:
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo ------------------------------------------------------------------------ From: garikoitz@gmail.com <mailto:garikoitz@gmail.com> Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com <mailto:pablonajt@hotmail.com> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt@hotmail.com <mailto:pablonajt@hotmail.com>> wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo ------------------------------------------------------------------------ From: pablonajt@hotmail.com <mailto:pablonajt@hotmail.com> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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
Thanks,Pablo
Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkaufman@nmr.mgh.harvard.edu To: garikoitz@gmail.com CC: pablonajt@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
I have to agree with Gari, I see no reason for you to not use the CentOS6 build.
-Zeke
On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote:
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo ------------------------------------------------------------------------ From: garikoitz@gmail.com <mailto:garikoitz@gmail.com> Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com <mailto:pablonajt@hotmail.com> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt@hotmail.com <mailto:pablonajt@hotmail.com>> wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo ------------------------------------------------------------------------ From: pablonajt@hotmail.com <mailto:pablonajt@hotmail.com> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am wondering up to how many recon -all for separate subjects I can run in parallel. With the version of Snow Leopard 32b I was running two at a time and it took around 20 hours. Would I be able to run 6 subjects in parallel? If so would this process still efficient or there is an optimum number?Thank you,Pablo
Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkaufman@nmr.mgh.harvard.edu To: garikoitz@gmail.com CC: pablonajt@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
I have to agree with Gari, I see no reason for you to not use the CentOS6 build.
-Zeke
On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote:
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo ------------------------------------------------------------------------ From: garikoitz@gmail.com <mailto:garikoitz@gmail.com> Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com <mailto:pablonajt@hotmail.com> CC: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt@hotmail.com <mailto:pablonajt@hotmail.com>> wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo ------------------------------------------------------------------------ From: pablonajt@hotmail.com <mailto:pablonajt@hotmail.com> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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
Hi Pablo
it depends on how many cores you have
Bruce On Thu, 21 Nov 2013, pablo najt wrote:
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am wondering up to how many recon -all for separate subjects I can run in parallel. With the version of Snow Leopard 32b I was running two at a time and it took around 20 hours. Would I be able to run 6 subjects in parallel? If so would this process still efficient or there is an optimum number? Thank you, Pablo
Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkaufman@nmr.mgh.harvard.edu To: garikoitz@gmail.com CC: pablonajt@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and
CentOS 6
I have to agree with Gari, I see no reason for you to not use the CentOS6 build.
-Zeke
On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote:
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user
:)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo
From: garikoitz@gmail.com mailto:garikoitz@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com mailto:pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234).
for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari
On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo
From: pablonajt@hotmail.com mailto:pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel).
I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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 mailto: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 mailto: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.
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Bruce Fischl -
Garikoitz Lerma-Usabiaga -
krista kelly -
pablo najt -
Watson, Christopher -
Z K