The information you request is in the attachments. Also I sent dmrirc.
Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis < jdavis@mrn.org> Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis jdavis@mrn.org Sent: Thursday, February 15, 2018 4:47:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
Hi Anastasia and John, This looks like the glibc issue that was fixed in more recent versions of FSL. Given that you are running Ubuntu 16.04, if you are using an older version of FSL, you will get FLIRT matrices saved in hexadecimal format. If you upgrade your FSL to a more recent version, you should be okay.
On Fri, Feb 16, 2018 at 2:10 AM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis < jdavis@mrn.org> *Sent:* Thursday, February 15, 2018 4:47:39 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis < jdavis@mrn.org> Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
Thanks for the tip! I hope that diff2anatorig.bbr.mat looks fine, however, because that one in particular comes from bbregister. Perhaps this glitch affected later steps.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Niels Bergsland theniels@gmail.com Sent: Friday, February 16, 2018 4:32:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Hi Anastasia and John, This looks like the glibc issue that was fixed in more recent versions of FSL. Given that you are running Ubuntu 16.04, if you are using an older version of FSL, you will get FLIRT matrices saved in hexadecimal format. If you upgrade your FSL to a more recent version, you should be okay.
On Fri, Feb 16, 2018 at 2:10 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Sent: Thursday, February 15, 2018 4:47:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Anastasia, Q: Do the other registration files look like this too? I'm glad you asked. I looked at the .mat files. Two of the mat files have regular numbers. The rest have hex. Also, many of the numbers in these files seem quite huge to me. The two mat files that look normal are anatorig2anat.mat and diff2anatorig.bbr.mat. I put some examples, including both hex and regular, in the attachment. I also put ".dat" and ".dat.sum". Those look normal, too.
Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
Once again thanks. John
On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis < jdavis@mrn.org> *Sent:* Thursday, February 15, 2018 4:47:39 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis < jdavis@mrn.org> Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
OK, so the ones that come from bbregister (a freesurfer tool) are fine. Then it's possible that this is related to the FSL glitch. It's worth trying. Sorry about this, I hope to reduce dependencies in the future.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis jdavis@mrn.org Sent: Friday, February 16, 2018 10:39:35 AM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Anastasia, Q: Do the other registration files look like this too? I'm glad you asked. I looked at the .mat files. Two of the mat files have regular numbers. The rest have hex. Also, many of the numbers in these files seem quite huge to me. The two mat files that look normal are anatorig2anat.mat and diff2anatorig.bbr.mat. I put some examples, including both hex and regular, in the attachment. I also put ".dat" and ".dat.sum". Those look normal, too.
Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
Once again thanks. John
On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Sent: Thursday, February 15, 2018 4:47:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
Anastasia, Great - this is awesome (knock on wood). Version 5.0.9 looks stable, but I should probably ask IT department for the recommended. Is that the latest stable version? John
On Fri, Feb 16, 2018 at 8:56 AM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
OK, so the ones that come from bbregister (a freesurfer tool) are fine. Then it's possible that this is related to the FSL glitch. It's worth trying. Sorry about this, I hope to reduce dependencies in the future.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis < jdavis@mrn.org> *Sent:* Friday, February 16, 2018 10:39:35 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Difficulties running tracula
Anastasia, Q: Do the other registration files look like this too? I'm glad you asked. I looked at the .mat files. Two of the mat files have regular numbers. The rest have hex. Also, many of the numbers in these files seem quite huge to me. The two mat files that look normal are anatorig2anat.mat and diff2anatorig.bbr.mat. I put some examples, including both hex and regular, in the attachment. I also put ".dat" and ".dat.sum". Those look normal, too.
Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
Once again thanks. John
On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis < jdavis@mrn.org> *Sent:* Thursday, February 15, 2018 4:47:39 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis < jdavis@mrn.org> Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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 again, The latest version is 5.0.10 but the issue was definitely fixed in 5.0.9 (possibly one point release earlier, I can't recall). Regardless, I don't think there were any changes to flirt between 5.0.9 and 5.0.10.
Good luck! Niels
On Fri, Feb 16, 2018 at 5:40 PM, John Davis jdavis@mrn.org wrote:
Anastasia, Great - this is awesome (knock on wood). Version 5.0.9 looks stable, but I should probably ask IT department for the recommended. Is that the latest stable version? John
On Fri, Feb 16, 2018 at 8:56 AM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
OK, so the ones that come from bbregister (a freesurfer tool) are fine. Then it's possible that this is related to the FSL glitch. It's worth trying. Sorry about this, I hope to reduce dependencies in the future.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis < jdavis@mrn.org> *Sent:* Friday, February 16, 2018 10:39:35 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Difficulties running tracula
Anastasia, Q: Do the other registration files look like this too? I'm glad you asked. I looked at the .mat files. Two of the mat files have regular numbers. The rest have hex. Also, many of the numbers in these files seem quite huge to me. The two mat files that look normal are anatorig2anat.mat and diff2anatorig.bbr.mat. I put some examples, including both hex and regular, in the attachment. I also put ".dat" and ".dat.sum". Those look normal, too.
Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
Once again thanks. John
On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis < jdavis@mrn.org> *Sent:* Thursday, February 15, 2018 4:47:39 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Davis < jdavis@mrn.org> Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
-- John Davis, PhD Cell: (520) 907-9769 jdavis@mrn.org
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.
Thanks for the info, Niels.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Niels Bergsland theniels@gmail.com Sent: Friday, February 16, 2018 3:38:56 PM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Hi again, The latest version is 5.0.10 but the issue was definitely fixed in 5.0.9 (possibly one point release earlier, I can't recall). Regardless, I don't think there were any changes to flirt between 5.0.9 and 5.0.10.
Good luck! Niels
On Fri, Feb 16, 2018 at 5:40 PM, John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> wrote: Anastasia, Great - this is awesome (knock on wood). Version 5.0.9 looks stable, but I should probably ask IT department for the recommended. Is that the latest stable version? John
On Fri, Feb 16, 2018 at 8:56 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
OK, so the ones that come from bbregister (a freesurfer tool) are fine. Then it's possible that this is related to the FSL glitch. It's worth trying. Sorry about this, I hope to reduce dependencies in the future.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Sent: Friday, February 16, 2018 10:39:35 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Anastasia, Q: Do the other registration files look like this too? I'm glad you asked. I looked at the .mat files. Two of the mat files have regular numbers. The rest have hex. Also, many of the numbers in these files seem quite huge to me. The two mat files that look normal are anatorig2anat.mat and diff2anatorig.bbr.mat. I put some examples, including both hex and regular, in the attachment. I also put ".dat" and ".dat.sum". Those look normal, too.
Also, Anastasia and Niels, the two most recent we have are fsl-5.0.1 and fsl-5.0.5. I set $FSLDIR to fsl-5.0.1.
Once again thanks. John
On Thu, Feb 15, 2018 at 6:10 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:
Sorry to hear. Do the other registration files in the dmri/xmfs/ directory, including diff2anatorig.bbr.mat, look like this too?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Sent: Thursday, February 15, 2018 4:47:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Difficulties running tracula
Anastasia, I tried your solution. "setenv LC_NUMERIC en_US.UTF-8" in the shell start up files. Unfortunately, it didn't work. I did it from both a tcsh and a bash shell. (local reasons for trying that). Neither worked. The outcome was identical, but I can send the files in again if you need. Thank you for helping John
On Wed, Feb 14, 2018 at 2:20 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi John – The problem is the funky format of the numbers in that registration file. It expects a 4x4 matrix of regular decimal numbers. Are the numbers in all the other registration files in the xfms/ directory in this same format? It probably has something to do with how your unix environment variables are set. Try "setenv LC_NUMERIC en_US.UTF-8”. Does this change the output?
Best, a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Davis <jdavis@mrn.orgmailto:jdavis@mrn.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, February 12, 2018 at 11:20 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Difficulties running tracula
The information you request is in the attachments. Also I sent dmrirc.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
-- John Davis, PhD Cell: (520) 907-9769tel:(520)%20907-9769 jdavis@mrn.orgmailto:jdavis@mrn.org
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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
-
John Davis -
Niels Bergsland -
Yendiki, Anastasia