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Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you
Are you sure this is the right recon-all.log file? At the end it says it finished without error
On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you
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You are correct. Attached is the correct one
On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you sure this is the right recon-all.log file? At the end it says it finished without error
On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:
External Email - Use CautionHell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag?
On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
You are correct. Attached is the correct one
On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you sure this is the right recon-all.log file? At the end it says it finished without error On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:External Email - Use Caution Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1peaI__TeJUbckv4J0VtL4MTLgh8HhDrvjWzEqk36JlsynZtg24NMdsXIrGSrC2d7PqTETC2uwSuSNCfa3J1QORMuqylPj2tK9MPuPZQSSaWL9Z-HtdKTmd06qo1I3nilcVlgjz51aUlBz7cZTMe5ApIg9Ep_pO4VmqmtH5Ulg99RZ-2ZE1vvuf9XVCaotO5Eh56KorgIk8Nc1J5POJB_VJ78DX7qZ0RI4Jdn7G6kqm_uLWKg12gvw2yezO4SYcbCpUyqjp8b4UJbWtFIFlwPCs8J7xQLXm5zsexbExdxrYNo46YYPzzCtJ5MTwZo1SqseAJUMytKw1rg1hrBW7VtDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1peaI__TeJUbckv4J0VtL4MTLgh8HhDrvjWzEqk36JlsynZtg24NMdsXIrGSrC2d7PqTETC2uwSuSNCfa3J1QORMuqylPj2tK9MPuPZQSSaWL9Z-HtdKTmd06qo1I3nilcVlgjz51aUlBz7cZTMe5ApIg9Ep_pO4VmqmtH5Ulg99RZ-2ZE1vvuf9XVCaotO5Eh56KorgIk8Nc1J5POJB_VJ78DX7qZ0RI4Jdn7G6kqm_uLWKg12gvw2yezO4SYcbCpUyqjp8b4UJbWtFIFlwPCs8J7xQLXm5zsexbExdxrYNo46YYPzzCtJ5MTwZo1SqseAJUMytKw1rg1hrBW7VtDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1h3Y3qTYqoxGlUZHbjHavv2tnOIkRi_rCMo0PBku7zhJqx2GUyYm-dBcu5aBjKWRXiUathDztGijy2UmZZMDOvKcZAGwLYBcAClqKklY_ojiX5JWwSZNPeCzHXyLsXAVb5u9A1RmZ7s3YTrwXEvO_h1ZPmZPk0_BsapJDqIWnXuhJ8MiaGYgqq8pB4ga8gJUAdDoJy9NN5OVF6jfWmcBaSpmMUnO9nC92VMpyrVp6xvodUGD6rfA1HLcAJ_t0kKb1k8CtY1qG2RX98LOhqpb6CsjiGw53YdHOkKnpIF2myhB6NlvXWVBcDay9ZgxrVvM53ntsgQTWLytOg3loXrlb4g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1h3Y3qTYqoxGlUZHbjHavv2tnOIkRi_rCMo0PBku7zhJqx2GUyYm-dBcu5aBjKWRXiUathDztGijy2UmZZMDOvKcZAGwLYBcAClqKklY_ojiX5JWwSZNPeCzHXyLsXAVb5u9A1RmZ7s3YTrwXEvO_h1ZPmZPk0_BsapJDqIWnXuhJ8MiaGYgqq8pB4ga8gJUAdDoJy9NN5OVF6jfWmcBaSpmMUnO9nC92VMpyrVp6xvodUGD6rfA1HLcAJ_t0kKb1k8CtY1qG2RX98LOhqpb6CsjiGw53YdHOkKnpIF2myhB6NlvXWVBcDay9ZgxrVvM53ntsgQTWLytOg3loXrlb4g/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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I actually can not remember how I got this specific output, I just sent it because of lack of info in the recon-all file. However, it stems from a problem I am encountering where I use a script to edit wm.mgz based on changes I make to filled.mgz. recon-all will fail at the same spot every time. I was able to fix the problem by running "mri_convert --in_like" on the wm.mgz using the original wm.mgz as the header reference. Attached is the recon-all.log for the failed recon-all. The puzzling thing is if I run mri_head on wm.mgz before and after mri_convert both have identical header information. I have attached the images. wm1.mgz is the output from my script and wm2.mgz is from mri_convert. Are you able to understand the difference in the files?
On Wed, Jan 8, 2025 at 8:01 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag?
On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:
External Email - Use CautionYou are correct. Attached is the correct one
On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Are you sure this is the right recon-all.log file? At the end it says it finished without error
On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:
External Email - Use CautionHell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you
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unless it is repeatable, it is really hard to debug
On 1/8/2025 6:57 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
I actually can not remember how I got this specific output, I just sent it because of lack of info in the recon-all file. However, it stems from a problem I am encountering where I use a script to edit wm.mgz based on changes I make to filled.mgz. recon-all will fail at the same spot every time. I was able to fix the problem by running "mri_convert --in_like" on the wm.mgz using the original wm.mgz as the header reference. Attached is the recon-all.log for the failed recon-all. The puzzling thing is if I run mri_head on wm.mgz before and after mri_convert both have identical header information. I have attached the images. wm1.mgz is the output from my script and wm2.mgz is from mri_convert. Are you able to understand the difference in the files?
On Wed, Jan 8, 2025 at 8:01 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag? On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:External Email - Use Caution You are correct. Attached is the correct one On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: Are you sure this is the right recon-all.log file? At the end it says it finished without error On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:External Email - Use Caution Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The recon-all log file looks fine. I was testing a situation where we edit the wm.mgz and filled.mgz at the same time then run recon-all with -autorecon-wm. Attached is the recon-all log file. It should have all relevant info of version and description of our system. Any help would be appreciated. Thank you _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1peaI__TeJUbckv4J0VtL4MTLgh8HhDrvjWzEqk36JlsynZtg24NMdsXIrGSrC2d7PqTETC2uwSuSNCfa3J1QORMuqylPj2tK9MPuPZQSSaWL9Z-HtdKTmd06qo1I3nilcVlgjz51aUlBz7cZTMe5ApIg9Ep_pO4VmqmtH5Ulg99RZ-2ZE1vvuf9XVCaotO5Eh56KorgIk8Nc1J5POJB_VJ78DX7qZ0RI4Jdn7G6kqm_uLWKg12gvw2yezO4SYcbCpUyqjp8b4UJbWtFIFlwPCs8J7xQLXm5zsexbExdxrYNo46YYPzzCtJ5MTwZo1SqseAJUMytKw1rg1hrBW7VtDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1peaI__TeJUbckv4J0VtL4MTLgh8HhDrvjWzEqk36JlsynZtg24NMdsXIrGSrC2d7PqTETC2uwSuSNCfa3J1QORMuqylPj2tK9MPuPZQSSaWL9Z-HtdKTmd06qo1I3nilcVlgjz51aUlBz7cZTMe5ApIg9Ep_pO4VmqmtH5Ulg99RZ-2ZE1vvuf9XVCaotO5Eh56KorgIk8Nc1J5POJB_VJ78DX7qZ0RI4Jdn7G6kqm_uLWKg12gvw2yezO4SYcbCpUyqjp8b4UJbWtFIFlwPCs8J7xQLXm5zsexbExdxrYNo46YYPzzCtJ5MTwZo1SqseAJUMytKw1rg1hrBW7VtDA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> The information in this e-mail is intended only for the person to whom it is addressed. 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