External Email - Use Caution
Hello to everyone!
I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error:
mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory
As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help!
Ioannis P.
Hi Ioannis - Any chance that you're running into this previously reported (and addressed) problem? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71427.html
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Pap mentadexx@gmail.com Sent: Sunday, January 16, 2022 5:40 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
External Email - Use Caution
Hello to everyone!
I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error:
mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory
As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help!
Ioannis P.
External Email - Use Caution
That is correct! I saved the fixed version of the trac-preproc but the problem still remained. Everything works fine when I run the preprocessing on more than one subject just like you mentioned. Any way to fix this? Thank you for your reply!
Ioannis P.
https://secure-web.cisco.com/1g7bt-cDndS7A6vih-VxCY9CSGUDM5PwOB9Oxi8EXZSFgPl5dxBAbF-zZuHZJvKgLG4snP78-9vBDJD9nj1CDmfwDNx9eYdAD9z_mGB2HZRN7D38WTmXCjg81plC_3kcy7XUio_PLOjZp98lYtd5tCFtr9lzVPUZ8RjPXvK5CmgWI4GsnjgmPvFPZ28ADqQ9HAx-IaJ0emCXQOVAq8S4QiLeTuyRpc3g2mfIksW7ldLDpm92Fxkbg6rwTnO2iiFRe7NKfRbYw021b0qYkcgW5DJKp6_35jUuFcNnjSbWi7dlPduygnNyjeCv4viinIZ_uM4z9-oOzJH-cSZp8aoZhmg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. http://secure-web.cisco.com/1-yFtbus3Qw8Hg0WakHaQ6JPQQj5A6LQWfsQAcnFUjOeFwjj... https://secure-web.cisco.com/1I81vc1_Bgueu_S1L2tfXvOJ8aoFne-kUcLDA3XPapOLg0kpPpABxro1p7r09V2jBPljSJAzKRy11fhW6eUlJMw0zIC3TV0-Zyl6GEj6tgrfyN7VDMpKBKValcGDpekXgW-n8uIIsrfGzYzuxrNP_HWULCdZi37PFQk0-H0_DQHFP7WKu58PNURfdTRpG1ZpQhJwt1jO_4TQrs4KpIZOC0nUp_3ioV-9a7XEKyUZCl_lc3-Q8EeBl1WHZzJT6cicQjBy6_O8NE6Fweqj3mtf3HdVo1_ZUTi_37uROE48DFROcmjxfOb9Lij2yGFhm1Hir4Z1MYiJF7yZU9JVxazz4jQ/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
On Thu, Jan 20, 2022 at 6:00 AM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Ioannis - Any chance that you're running into this previously reported (and addressed) problem? https://secure-web.cisco.com/14FAyoW83tF041YujgFuIkKvWm2U1SkX38EM1ORa0xOxCbc...
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Pap < mentadexx@gmail.com> *Sent:* Sunday, January 16, 2022 5:40 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
External Email - Use CautionHello to everyone!
I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error:
mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory
As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help!
Ioannis P. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1P9CML8ExidnuK-FItSfKSp2NdEVd1G6N348i0oTDujNAUP... 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 http://secure-web.cisco.com/14OfonVMiIgifL8X0MQt9XWUBTPjads8-PcRSR5fZdxbsuQS... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Hi Ioannis - When you run "which trac-preproc" on the command line, is the path that you see the same as the location where you saved the new trac-preproc?
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of John Pap mentadexx@gmail.com Sent: Friday, January 21, 2022 10:55 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
External Email - Use Caution
That is correct! I saved the fixed version of the trac-preproc but the problem still remained. Everything works fine when I run the preprocessing on more than one subject just like you mentioned. Any way to fix this? Thank you for your reply!
Ioannis P.
[https://secure-web.cisco.com/1x-f6gViE6AZ8_o0hj6IEq6Le1w_BfF25VS0uPB8ipFLoNo...]https://secure-web.cisco.com/1g7bt-cDndS7A6vih-VxCY9CSGUDM5PwOB9Oxi8EXZSFgPl5dxBAbF-zZuHZJvKgLG4snP78-9vBDJD9nj1CDmfwDNx9eYdAD9z_mGB2HZRN7D38WTmXCjg81plC_3kcy7XUio_PLOjZp98lYtd5tCFtr9lzVPUZ8RjPXvK5CmgWI4GsnjgmPvFPZ28ADqQ9HAx-IaJ0emCXQOVAq8S4QiLeTuyRpc3g2mfIksW7ldLDpm92Fxkbg6rwTnO2iiFRe7NKfRbYw021b0qYkcgW5DJKp6_35jUuFcNnjSbWi7dlPduygnNyjeCv4viinIZ_uM4z9-oOzJH-cSZp8aoZhmg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.avast.comhttps://secure-web.cisco.com/1I81vc1_Bgueu_S1L2tfXvOJ8aoFne-kUcLDA3XPapOLg0kpPpABxro1p7r09V2jBPljSJAzKRy11fhW6eUlJMw0zIC3TV0-Zyl6GEj6tgrfyN7VDMpKBKValcGDpekXgW-n8uIIsrfGzYzuxrNP_HWULCdZi37PFQk0-H0_DQHFP7WKu58PNURfdTRpG1ZpQhJwt1jO_4TQrs4KpIZOC0nUp_3ioV-9a7XEKyUZCl_lc3-Q8EeBl1WHZzJT6cicQjBy6_O8NE6Fweqj3mtf3HdVo1_ZUTi_37uROE48DFROcmjxfOb9Lij2yGFhm1Hir4Z1MYiJF7yZU9JVxazz4jQ/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink
On Thu, Jan 20, 2022 at 6:00 AM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Ioannis - Any chance that you're running into this previously reported (and addressed) problem? MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg71427.htmlhttps://secure-web.cisco.com/14FAyoW83tF041YujgFuIkKvWm2U1SkX38EM1ORa0xOxCbcLOqulVZDLPwC1A9nWWp_PSQCrFuYzg1rAytsxJtaQDwZbCP442PS2Z-8LxQZ2PkVP_BOFaDqtmlljttVtXLt-3ElOVqyQAc04XRndM14Oh4VyZzZNMz6ljtN7Nyft84lPWovueRLeO0WPWq_d0muaRs2NQXCyZV089z5IJeNdYJ551MPdKd7US-efkcKaH-JuAjgLMQYJZhce3ChiGoMTOz1o6EN5hPdBDu_o6KYlfjO7Z-9hHSnRJmkmUZOEeYqnS9bOKnWRGM6FNK5xWFvwRJ5z-u8b7EttntVQm-g/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71427.html
Anastasia. ________________________________ 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 Pap <mentadexx@gmail.commailto:mentadexx@gmail.com> Sent: Sunday, January 16, 2022 5:40 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
External Email - Use Caution
Hello to everyone!
I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error:
mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory
As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help!
Ioannis P. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1P9CML8ExidnuK-FItSfKSp2NdEVd1G6N348i0oTDujNAUPCwa6x24zjZGqvuUX0V-2zuj8Od7x0fpC3c0L9RR0SIBmUzOANPVwXMfAmX4Hddl6Ru_71I5MH9W__LOMIbAoj8YWAh0oiyRj_6UQGr988OnQblTNl8nW0750r7ZUOrW6T6TrT8QUOqvJXhf6lAte52kNhtzTxZwMD-xy2NREyyztPZ5A63222LVMV5E-5px8XCB8pMLOiVGCHScFmhGA1O7SQWiLgJnQv0nRcltl1WcqRlaAK1_M5As_Tvmkn_jYFGWeGm51rR6tZ5XvI5mh4jJBvQQCRM2db_KUISlw/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 http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/14OfonVMiIgifL8X0MQt9XWUBTPjads8-PcRSR5fZdxbsuQS9D8rJ4QK856GQehVGjrzevOj7oMmMaAwsJDqfUJyvuvFj3skmCMjJq1h6M0GYGqMhrohPpaP_QHNYJ2Qbo5jjxZOrTwe8WuWbbHOW5UhO1HnJGPUQrtwfW9MXKz5OEeh5FjomJEUAJS58igIndDdLjR5nlxKZXfZfv4NpLtlnMcleieJEPEnUJY3uz0AxCQZYCdUy0rbEctWnfB7SpYDlWdKScHypbNX_ueaMxfv3SD6qWxXbvaCJ4rd0Xq8MoOMCi5ZZ5hdYAHLjOQkGhn7v7FYcGEF191KwSyUw7A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
Hi Anastasia!
I copied the contents of the fixed version directly to the trac-preproc file located in the bin and then saved it there. I attach the file located in the bin folder of freesurfer just in case I did something wrong. Thanks!
Ioannis P.
https://secure-web.cisco.com/1eDOja40m2xnCFJyqacmrXr3Mxv7AgXBqNLU6ZogNPsV4ypL_VmDFT3ovsPi3F2KEn2tRYm9WJ7RGvNEp3e51R-NpDGnMjfM7t1Sm463s7pnbipErSId2uXnaoIcahNp1HI67H_i4OOIkIXvVjruZPT490yDqrz1NpJSu3YcdlVZwj6yQMja7lN-_6k_lHGqqB6RsAyxCp4GI8U6KUOYigPMf-mqa6WxEu_sk_bifQ7jkIn9tRctkjDubeAdZraiAOTAxPOfo4FEXcGnH-NXbRH8jWfr8UFOzO51VvH-rjkzkJ_CMWbZIIiy7WyXCr8RgXk3pjqSeCJtSOeiOH1vS7w/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. http://secure-web.cisco.com/1deH_z_inMlWKieiW-NoXxiNJsj_JPyFwKg6ryi-2pRfhCLb... https://secure-web.cisco.com/1hkFX8ywsE3EnObDsfoMMV35bbXDbuKm9AsWsBTFENwQ2pWI-uinZxUtRAy2DFrKJkCPK569-sb_bW92m1qeMLllrCgMRDxWiWvevIrVqJ0wSO9jtgGK6OY_6lPZkWNpwVmpOouacfR6spyRgY6NEY5F15Xmue-THETbVPURs4JMxaufOFnXbgDzSHA3YO-itHg2HBu8LBRHE6tlXrnyLdoiuD40zDfz1mNte-xITjF7kigp3-lDSchLH7EhFp-Q-oNLmQsl5YCaQXjya8VFHAjlaHLmOTDaB2DU-sBYSx-dlRCa1pHbhJ6w2CLlM9tOsmzhcYwZGWcfAviEvIkUKeA/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
On Fri, Jan 21, 2022 at 7:54 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Ioannis - When you run "which trac-preproc" on the command line, is the path that you see the same as the location where you saved the new trac-preproc?
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Pap < mentadexx@gmail.com> *Sent:* Friday, January 21, 2022 10:55 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
External Email - Use CautionThat is correct! I saved the fixed version of the trac-preproc but the problem still remained. Everything works fine when I run the preprocessing on more than one subject just like you mentioned. Any way to fix this? Thank you for your reply!
Ioannis P.
https://secure-web.cisco.com/1g7bt-cDndS7A6vih-VxCY9CSGUDM5PwOB9Oxi8EXZSFgPl5dxBAbF-zZuHZJvKgLG4snP78-9vBDJD9nj1CDmfwDNx9eYdAD9z_mGB2HZRN7D38WTmXCjg81plC_3kcy7XUio_PLOjZp98lYtd5tCFtr9lzVPUZ8RjPXvK5CmgWI4GsnjgmPvFPZ28ADqQ9HAx-IaJ0emCXQOVAq8S4QiLeTuyRpc3g2mfIksW7ldLDpm92Fxkbg6rwTnO2iiFRe7NKfRbYw021b0qYkcgW5DJKp6_35jUuFcNnjSbWi7dlPduygnNyjeCv4viinIZ_uM4z9-oOzJH-cSZp8aoZhmg/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon Virus-free. *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1deH_z_inMlWKieiW-NoXxiNJsj_JPyFwKg6ryi-2pRfhCLb... https://secure-web.cisco.com/1I81vc1_Bgueu_S1L2tfXvOJ8aoFne-kUcLDA3XPapOLg0kpPpABxro1p7r09V2jBPljSJAzKRy11fhW6eUlJMw0zIC3TV0-Zyl6GEj6tgrfyN7VDMpKBKValcGDpekXgW-n8uIIsrfGzYzuxrNP_HWULCdZi37PFQk0-H0_DQHFP7WKu58PNURfdTRpG1ZpQhJwt1jO_4TQrs4KpIZOC0nUp_3ioV-9a7XEKyUZCl_lc3-Q8EeBl1WHZzJT6cicQjBy6_O8NE6Fweqj3mtf3HdVo1_ZUTi_37uROE48DFROcmjxfOb9Lij2yGFhm1Hir4Z1MYiJF7yZU9JVxazz4jQ/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink <#m_-4084420060666021480_m_-3336443154814653608_x_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
On Thu, Jan 20, 2022 at 6:00 AM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Hi Ioannis - Any chance that you're running into this previously reported (and addressed) problem? *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1DOTOlBpTB6xuoSlzx00BcuQAQz_QlLHKmKpGPs8q4kFer7... https://secure-web.cisco.com/14FAyoW83tF041YujgFuIkKvWm2U1SkX38EM1ORa0xOxCbcLOqulVZDLPwC1A9nWWp_PSQCrFuYzg1rAytsxJtaQDwZbCP442PS2Z-8LxQZ2PkVP_BOFaDqtmlljttVtXLt-3ElOVqyQAc04XRndM14Oh4VyZzZNMz6ljtN7Nyft84lPWovueRLeO0WPWq_d0muaRs2NQXCyZV089z5IJeNdYJ551MPdKd7US-efkcKaH-JuAjgLMQYJZhce3ChiGoMTOz1o6EN5hPdBDu_o6KYlfjO7Z-9hHSnRJmkmUZOEeYqnS9bOKnWRGM6FNK5xWFvwRJ5z-u8b7EttntVQm-g/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg71427.html
Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of John Pap < mentadexx@gmail.com> *Sent:* Sunday, January 16, 2022 5:40 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
External Email - Use CautionHello to everyone!
I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error:
mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory
As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help!
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John Pap -
Yendiki, Anastasia