External Email - Use Caution
I don’t see an error message in what you posted below. I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges. -R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sg> wrote: External Email - Use Caution Hi, I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.The stage where it stops#@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023The error that was in the error log.CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mghWhat should I do to resolve this issue? Cheers,Mervin Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fsbuild fsbuild@contbay.com Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Mervin Tee mervintee@nus.edu.sg Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
- External Email -
External Email - Use Caution
I don’t see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee mervintee@nus.edu.sg wrote:
External Email - Use Caution
Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh
What should I do to resolve this issue?
Cheers, Mervin
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. _______________________________________________ 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://secure-web.cisco.com/1MU2qXahcAIDTGuNOIYvfaxhNt_RHzW_dnBucZmQt9JwJK_...https://secure-web.cisco.com/1FZd4cRvMJaVYQC3s_7vhvZrDnHhyJSq6ZpDFW5OppcooF4NkoM9HbMpY4AU4ozoi4oHj9ns12VNnlSNWhI9CipTbhqvYBM6y73mOGdB0J1h4wNa5wDv7SyUcOg6epDZ8NDdmWDu_c7dYv3bWLG9rHAJRvVpoagTWYrD1h3Mi7nCMeXbRad3iS7BuFoKOVJXY5D69ZATO8iN-EiM_Q2lb6AHFMSWd0lS1eetBXlDW2NaWwQ7ECDpdULruS_DSNTGaX5e3xwaLH7EKE9oq9OS3mTIwacwJ9tnTMW-1t5vMmLq00zy4sdDpvXXNXHdR9UHS/https%3A%2F%2Fddec1-0-en-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1IO3u8TmP17OQfIG2beUfwjpisQihIq2KAEj37EkOmeU8dqNnRDA8Q0l1vRxZaWUktIPiOnVd9z2Vthsiq60E3E74ep0BvEFmJTh3eZLVpPAyct3E7CfGy8eTRVXScBQE6UZpQkblvNPUN69CKbO6AX54%255f1uuvIK5G1unQnknF8y1zXgBKllrTG2KKsfDLrk7XA9mR7SUz9vjrbY2ARnuqF3jPZo%255fMvWEABNXgA%255fG34Y6iaWCvJlhkB%255f60eprJBBWyD5s2Q2Pc6Q%255fxf4q2ORhSdOJOiwyQ3av3pr2iTABSvR%255fSGVkg3bLFyzuZn2UtpR9W4JMhw8lSLIga5t6P8bZQg%252fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26umid%3Df432ea85-a7ec-484a-a559-ff96c2b6828e%26auth%3D8d3ccd473d52f326e51c0f75cb32c9541898e5d5-aa05409f729694bd38c0f3b53f7ff1d9f61f682f
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
External Email - Use Caution
Can you send the recon-all.log?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mervin Tee Sent: Monday, September 25, 2023 2:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________ 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 fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
- External Email -
External Email - Use Caution
I don't see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> wrote:
External Email - Use Caution
Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh What should I do to resolve this issue?
Cheers, Mervin
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. _______________________________________________ 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://secure-web.cisco.com/1jkJ9Q-_kOAhy21gYRKrZThreLX5f-WOy0iAosoMFapOJNO...https://secure-web.cisco.com/1FZd4cRvMJaVYQC3s_7vhvZrDnHhyJSq6ZpDFW5OppcooF4NkoM9HbMpY4AU4ozoi4oHj9ns12VNnlSNWhI9CipTbhqvYBM6y73mOGdB0J1h4wNa5wDv7SyUcOg6epDZ8NDdmWDu_c7dYv3bWLG9rHAJRvVpoagTWYrD1h3Mi7nCMeXbRad3iS7BuFoKOVJXY5D69ZATO8iN-EiM_Q2lb6AHFMSWd0lS1eetBXlDW2NaWwQ7ECDpdULruS_DSNTGaX5e3xwaLH7EKE9oq9OS3mTIwacwJ9tnTMW-1t5vMmLq00zy4sdDpvXXNXHdR9UHS/https%3A%2F%2Fddec1-0-en-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1IO3u8TmP17OQfIG2beUfwjpisQihIq2KAEj37EkOmeU8dqNnRDA8Q0l1vRxZaWUktIPiOnVd9z2Vthsiq60E3E74ep0BvEFmJTh3eZLVpPAyct3E7CfGy8eTRVXScBQE6UZpQkblvNPUN69CKbO6AX54%255f1uuvIK5G1unQnknF8y1zXgBKllrTG2KKsfDLrk7XA9mR7SUz9vjrbY2ARnuqF3jPZo%255fMvWEABNXgA%255fG34Y6iaWCvJlhkB%255f60eprJBBWyD5s2Q2Pc6Q%255fxf4q2ORhSdOJOiwyQ3av3pr2iTABSvR%255fSGVkg3bLFyzuZn2UtpR9W4JMhw8lSLIga5t6P8bZQg%252fhttps%25253A%25252F%25252Fmail.nmr.mgh.harvard.edu%25252Fmailman%25252Flistinfo%25252Ffreesurfer%26umid%3Df432ea85-a7ec-484a-a559-ff96c2b6828e%26auth%3D8d3ccd473d52f326e51c0f75cb32c9541898e5d5-aa05409f729694bd38c0f3b53f7ff1d9f61f682f
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
External Email - Use Caution
HI Yujing,
Here's the log file you have requested. Do take note that I have followed a post to modify my recon-all from ln to cp. so, the commands might look different.
Cheers, Mervin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: 25 September 2023 20:49 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
- External Email -
External Email - Use Caution
Can you send the recon-all.log?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mervin Tee Sent: Monday, September 25, 2023 2:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution
Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________
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 fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
- External Email -
External Email - Use Caution
I don’t see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> wrote:
External Email - Use Caution
Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh
What should I do to resolve this issue?
Cheers,
Mervin
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. _______________________________________________ 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://secure-web.cisco.com/1F0wjt7WkL2kfYSPA121f4248ornn_BXDAlhp16r6bVGh6S...https://secure-web.cisco.com/1WQa6-QYo7CLG38RjaZXEy1kHc1Qc5FCSUUVmVJ481k44DJOmWoYccUh-gc2SfqwmvltRplAcJm8JhEEjuECoMhx417JW_IazlotEkBq5MUt8TNVkes2lS9sRuDRahE1CoaxWZfgFpjuccMu1e_1SIdHZlrncDopVlLbEel5HiDH8PidT-3xaW0Y1r9uONMOzIR7Oq7CebNJyYYwHUKY56zQuGWUstESlD69Zizl2kZIaEfxLDmcxlAW9bQrMcuakIGyZ3JRxGlyRi4_H12AcfcMpjQgrJdcf3gtVmk3S5oQwYKGXpvkogxx-CvcQ0SdofRadGbWTiQ_ei5qQ9eiEPg/https%3A%2F%2Fddec1-0-en-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1FZd4cRvMJaVYQC3s%255f7vhvZrDnHhyJSq6ZpDFW5OppcooF4NkoM9HbMpY4AU4ozoi4oHj9ns12VNnlSNWhI9CipTbhqvYBM6y73mOGdB0J1h4wNa5wDv7SyUcOg6epDZ8NDdmWDu%255fc7dYv3bWLG9rHAJRvVpoagTWYrD1h3Mi7nCMeXbRad3iS7BuFoKOVJXY5D69ZATO8iN%252dEiM%255fQ2lb6AHFMSWd0lS1eetBXlDW2NaWwQ7ECDpdULruS%255fDSNTGaX5e3xwaLH7EKE9oq9OS3mTIwacwJ9tnTMW%252d1t5vMmLq00zy4sdDpvXXNXHdR9UHS%252fhttps%25253A%25252F%25252Fddec1%252d0%252den%252dctp.trendmicro.com%25253A443%25252Fwis%25252Fclicktime%25252Fv1%25252Fquery%25253Furl%25253Dhttps%2525253a%2525252f%2525252fsecure%2525252dweb.cisco.com%2525252f1IO3u8TmP17OQfIG2beUfwjpisQihIq2KAEj37EkOmeU8dqNnRDA8Q0l1vRxZaWUktIPiOnVd9z2Vthsiq60E3E74ep0BvEFmJTh3eZLVpPAyct3E7CfGy8eTRVXScBQE6UZpQkblvNPUN69CKbO6AX54%2525255f1uuvIK5G1unQnknF8y1zXgBKllrTG2KKsfDLrk7XA9mR7SUz9vjrbY2ARnuqF3jPZo%2525255fMvWEABNXgA%2525255fG34Y6iaWCvJlhkB%2525255f60eprJBBWyD5s2Q2Pc6Q%2525255fxf4q2ORhSdOJOiwyQ3av3pr2iTABSvR%2525255fSGVkg3bLFyzuZn2UtpR9W4JMhw8lSLIga5t6P8bZQg%2525252fhttps%252525253A%252525252F%252525252Fmail.nmr.mgh.harvard.edu%252525252Fmailman%252525252Flistinfo%252525252Ffreesurfer%252526umid%25253Df432ea85%252da7ec%252d484a%252da559%252dff96c2b6828e%252526auth%25253D8d3ccd473d52f326e51c0f75cb32c9541898e5d5%252daa05409f729694bd38c0f3b53f7ff1d9f61f682f%26umid%3D2f0588e1-6dc2-4e78-9321-45a3d6060b22%26auth%3D8d3ccd473d52f326e51c0f75cb32c9541898e5d5-22db823c25e89e111063f0cc7607c6685a7cbad9
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
External Email - Use Caution
The error says "ERROR: cannot find /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/lh.white.K".
Can you send what your subject surf/ directory looks like - 'ls -lt /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/'?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mervin Tee Sent: Monday, September 25, 2023 9:39 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution HI Yujing,
Here's the log file you have requested. Do take note that I have followed a post to modify my recon-all from ln to cp. so, the commands might look different.
Cheers, Mervin
________________________________ 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 Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: 25 September 2023 20:49 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
- External Email -
External Email - Use Caution
Can you send the recon-all.log?
Yujing
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 Mervin Tee Sent: Monday, September 25, 2023 2:53 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution
Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________
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 fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
- External Email -
External Email - Use Caution
I don't see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> wrote:
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Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh
What should I do to resolve this issue?
Cheers,
Mervin
________________________________
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Hi Yujing,
You can find the directory listed before, however, before you start heading down the wrong path of this error. I have and am able to complete recon-all with no issue on my internal ssd that is formatted to work with symlink.
ls /media/mt/Expansion/Disk9/EDIS_751_alreadytrftoFS/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/ autodet.gw.stats.lh.dat lh.volume autodet.gw.stats.rh.dat lh.volume.fsaverage.mgh lh.area lh.volume.fsaverage.mris_preproc.log lh.area.fsaverage.mgh lh.w-g.pct.mgh lh.area.fsaverage.mris_preproc.log lh.white lh.area.mid lh.white.preaparc lh.area.pial lh.white.preaparc.H lh.area.pial.fsaverage.mgh lh.white.preaparc.K lh.area.pial.fsaverage.mris_preproc.log rh.area lh.avg_curv rh.area.mid lh.curv rh.area.pial lh.curv.fsaverage.mgh rh.avg_curv lh.curv.fsaverage.mris_preproc.log rh.curv lh.curv.pial rh.curv.pial lh.defect_borders rh.defect_borders lh.defect_chull rh.defect_chull lh.defect_labels rh.defect_labels lh.defects.pointset rh.defects.pointset lh.fsaverage.sphere.reg rh.fsaverage.sphere.reg lh.inflated rh.inflated lh.inflated.nofix rh.inflated.nofix lh.jacobian_white rh.jacobian_white lh.orig rh.orig lh.orig.nofix rh.orig.nofix lh.orig.premesh rh.orig.premesh lh.pial rh.pial lh.pial.T1 rh.pial.T1 lh.qsphere.nofix rh.qsphere.nofix lh.smoothwm rh.smoothwm lh.smoothwm.BE.crv rh.smoothwm.BE.crv lh.smoothwm.C.crv rh.smoothwm.C.crv lh.smoothwm.FI.crv rh.smoothwm.FI.crv lh.smoothwm.H.crv rh.smoothwm.H.crv lh.smoothwm.K1.crv rh.smoothwm.K1.crv lh.smoothwm.K2.crv rh.smoothwm.K2.crv lh.smoothwm.K.crv rh.smoothwm.K.crv lh.smoothwm.nofix rh.smoothwm.nofix lh.smoothwm.S.crv rh.smoothwm.S.crv lh.sphere rh.sphere lh.sphere.reg rh.sphere.reg lh.sulc rh.sulc lh.sulc.fsaverage.mgh rh.thickness lh.sulc.fsaverage.mris_preproc.log rh.volume lh.thickness rh.w-g.pct.mgh lh.thickness.fsaverage.mgh rh.white lh.thickness.fsaverage.mris_preproc.log rh.white.preaparc
Cheers, Mervin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: 25 September 2023 21:43 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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The error says “ERROR: cannot find /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/lh.white.K”.
Can you send what your subject surf/ directory looks like - ‘ls -lt /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/’?
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mervin Tee Sent: Monday, September 25, 2023 9:39 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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HI Yujing,
Here's the log file you have requested. Do take note that I have followed a post to modify my recon-all from ln to cp. so, the commands might look different.
Cheers, Mervin
________________________________
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 Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: 25 September 2023 20:49 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Can you send the recon-all.log?
Yujing
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 Mervin Tee Sent: Monday, September 25, 2023 2:53 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________
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 fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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I don’t see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> wrote:
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Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh
What should I do to resolve this issue?
Cheers,
Mervin
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. _______________________________________________ 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://secure-web.cisco.com/16w5zBSQEEIwQfwrpXzzBWhzMRiZ05gCswDTOdjemE66r8R...https://secure-web.cisco.com/1jUjS9URn0TDrVDj7NxOU4XmrListW4OD7-S02Vkb56daEa0Z7UelKgPghQxnevk3-GVAB-vRAHy6zx4Lm2TqLQcPshiOD4DxEj_Jb3vyWYjsvUgIv0vqWowsYN4YHUgwznDoMiYfFxMdS3L6JmQK5mLQby-8GB9yciVNK5WRx709IQLVHyF1Emq8BQ5mhSH5F13D2tsBn75P0DI2IeXtorMOVIbG9_exm4ytSddOt6BWcZzc9UT9zeUzFSWZI0OLyG1Doir2tygVotul_gaiFQ/https%3A%2F%2Fddec1-0-en-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1WQa6%252dQYo7CLG38RjaZXEy1kHc1Qc5FCSUUVmVJ481k44DJOmWoYccUh%252dgc2SfqwmvltRplAcJm8JhEEjuECoMhx417JW%255fIazlotEkBq5MUt8TNVkes2lS9sRuDRahE1CoaxWZfgFpjuccMu1e%255f1SIdHZlrncDopVlLbEel5HiDH8PidT%252d3xaW0Y1r9uONMOzIR7Oq7CebNJyYYwHUKY56zQuGWUstESlD69Zizl2kZIaEfxLDmcxlAW9bQrMcuakIGyZ3JRxGlyRi4%255fH12AcfcMpjQgrJdcf3gtVmk3S5oQwYKGXpvkogxx%252dCvcQ0SdofRadGbWTiQ%255fei5qQ9eiEPg%252fhttps%25253A%25252F%25252Fddec1%252d0%252den%252dctp.trendmicro.com%25253A443%25252Fwis%25252Fclicktime%25252Fv1%25252Fquery%25253Furl%25253Dhttps%2525253a%2525252f%2525252fsecure%2525252dweb.cisco.com%2525252f1FZd4cRvMJaVYQC3s%2525255f7vhvZrDnHhyJSq6ZpDFW5OppcooF4NkoM9HbMpY4AU4ozoi4oHj9ns12VNnlSNWhI9CipTbhqvYBM6y73mOGdB0J1h4wNa5wDv7SyUcOg6epDZ8NDdmWDu%2525255fc7dYv3bWLG9rHAJRvVpoagTWYrD1h3Mi7nCMeXbRad3iS7BuFoKOVJXY5D69ZATO8iN%2525252dEiM%2525255fQ2lb6AHFMSWd0lS1eetBXlDW2NaWwQ7ECDpdULruS%2525255fDSNTGaX5e3xwaLH7EKE9oq9OS3mTIwacwJ9tnTMW%2525252d1t5vMmLq00zy4sdDpvXXNXHdR9UHS%2525252fhttps%252525253A%252525252F%252525252Fddec1%2525252d0%2525252den%2525252dctp.trendmicro.com%252525253A443%252525252Fwis%252525252Fclicktime%252525252Fv1%252525252Fquery%252525253Furl%252525253Dhttps%25252525253a%25252525252f%25252525252fsecure%25252525252dweb.cisco.com%25252525252f1IO3u8TmP17OQfIG2beUfwjpisQihIq2KAEj37EkOmeU8dqNnRDA8Q0l1vRxZaWUktIPiOnVd9z2Vthsiq60E3E74ep0BvEFmJTh3eZLVpPAyct3E7CfGy8eTRVXScBQE6UZpQkblvNPUN69CKbO6AX54%25252525255f1uuvIK5G1unQnknF8y1zXgBKllrTG2KKsfDLrk7XA9mR7SUz9vjrbY2ARnuqF3jPZo%25252525255fMvWEABNXgA%25252525255fG34Y6iaWCvJlhkB%25252525255f60eprJBBWyD5s2Q2Pc6Q%25252525255fxf4q2ORhSdOJOiwyQ3av3pr2iTABSvR%25252525255fSGVkg3bLFyzuZn2UtpR9W4JMhw8lSLIga5t6P8bZQg%25252525252fhttps%2525252525253A%2525252525252F%2525252525252Fmail.nmr.mgh.harvard.edu%2525252525252Fmailman%2525252525252Flistinfo%2525252525252Ffreesurfer%2525252526umid%252525253Df432ea85%2525252da7ec%2525252d484a%2525252da559%2525252dff96c2b6828e%2525252526auth%252525253D8d3ccd473d52f326e51c0f75cb32c9541898e5d5%2525252daa05409f729694bd38c0f3b53f7ff1d9f61f682f%252526umid%25253D2f0588e1%252d6dc2%252d4e78%252d9321%252d45a3d6060b22%252526auth%25253D8d3ccd473d52f326e51c0f75cb32c9541898e5d5%252d22db823c25e89e111063f0cc7607c6685a7cbad9%26umid%3D748b1618-24f7-40a1-ba7b-91731af2704d%26auth%3D8d3ccd473d52f326e51c0f75cb32c9541898e5d5-653da3b7cf71945c70a092f53122dbce68dbf283
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lh.white.K and lh.white.H normally created as links to lh.white.preaparc.K and lh.white.preaparc.H
I don't see 'lh.white.K' in your surf/ directory either as a file or a symbolic link.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mervin Tee Sent: Monday, September 25, 2023 10:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
External Email - Use Caution Hi Yujing,
You can find the directory listed before, however, before you start heading down the wrong path of this error. I have and am able to complete recon-all with no issue on my internal ssd that is formatted to work with symlink.
ls /media/mt/Expansion/Disk9/EDIS_751_alreadytrftoFS/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/ autodet.gw.stats.lh.dat lh.volume autodet.gw.stats.rh.dat lh.volume.fsaverage.mgh lh.area lh.volume.fsaverage.mris_preproc.log lh.area.fsaverage.mgh lh.w-g.pct.mgh lh.area.fsaverage.mris_preproc.log lh.white lh.area.mid lh.white.preaparc lh.area.pial lh.white.preaparc.H lh.area.pial.fsaverage.mgh lh.white.preaparc.K lh.area.pial.fsaverage.mris_preproc.log rh.area lh.avg_curv rh.area.mid lh.curv rh.area.pial lh.curv.fsaverage.mgh rh.avg_curv lh.curv.fsaverage.mris_preproc.log rh.curv lh.curv.pial rh.curv.pial lh.defect_borders rh.defect_borders lh.defect_chull rh.defect_chull lh.defect_labels rh.defect_labels lh.defects.pointset rh.defects.pointset lh.fsaverage.sphere.reg rh.fsaverage.sphere.reg lh.inflated rh.inflated lh.inflated.nofix rh.inflated.nofix lh.jacobian_white rh.jacobian_white lh.orig rh.orig lh.orig.nofix rh.orig.nofix lh.orig.premesh rh.orig.premesh lh.pial rh.pial lh.pial.T1 rh.pial.T1 lh.qsphere.nofix rh.qsphere.nofix lh.smoothwm rh.smoothwm lh.smoothwm.BE.crv rh.smoothwm.BE.crv lh.smoothwm.C.crv rh.smoothwm.C.crv lh.smoothwm.FI.crv rh.smoothwm.FI.crv lh.smoothwm.H.crv rh.smoothwm.H.crv lh.smoothwm.K1.crv rh.smoothwm.K1.crv lh.smoothwm.K2.crv rh.smoothwm.K2.crv lh.smoothwm.K.crv rh.smoothwm.K.crv lh.smoothwm.nofix rh.smoothwm.nofix lh.smoothwm.S.crv rh.smoothwm.S.crv lh.sphere rh.sphere lh.sphere.reg rh.sphere.reg lh.sulc rh.sulc lh.sulc.fsaverage.mgh rh.thickness lh.sulc.fsaverage.mris_preproc.log rh.volume lh.thickness rh.w-g.pct.mgh lh.thickness.fsaverage.mgh rh.white lh.thickness.fsaverage.mris_preproc.log rh.white.preaparc
Cheers, Mervin
________________________________ 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 Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: 25 September 2023 21:43 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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The error says "ERROR: cannot find /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/lh.white.K".
Can you send what your subject surf/ directory looks like - 'ls -lt /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/'?
Yujing
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 Mervin Tee Sent: Monday, September 25, 2023 9:39 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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HI Yujing,
Here's the log file you have requested. Do take note that I have followed a post to modify my recon-all from ln to cp. so, the commands might look different.
Cheers, Mervin
________________________________
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 Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: 25 September 2023 20:49 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Can you send the recon-all.log?
Yujing
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 Mervin Tee Sent: Monday, September 25, 2023 2:53 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________
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 fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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I don't see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> wrote:
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Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh
What should I do to resolve this issue?
Cheers,
Mervin
________________________________
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Hi Yujing,
I think you are not understanding the question/issue I'm asking. I am aware that they are not creating links of those files and that it will be generated when it reaches these steps.
My folders are located on an exFAT drive. The symbolic link cannot be created due to exFAT format. Hence, my question isn't about whether lh.white.K is created or not or if it was missing from directory that causes it to be missing.
The question that I'm asking is if there's a solution to workaround external drives that are formatted as exFAT? As symbolic links can't be generated on exFAT formatted drives. Hope that clarifies.
Cheers, Mervin
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@MGH.HARVARD.EDU Sent: 25 September 2023 22:17 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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lh.white.K and lh.white.H normally created as links to lh.white.preaparc.K and lh.white.preaparc.H
I don’t see ‘lh.white.K’ in your surf/ directory either as a file or a symbolic link.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Mervin Tee Sent: Monday, September 25, 2023 10:03 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Hi Yujing,
You can find the directory listed before, however, before you start heading down the wrong path of this error. I have and am able to complete recon-all with no issue on my internal ssd that is formatted to work with symlink.
ls /media/mt/Expansion/Disk9/EDIS_751_alreadytrftoFS/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/
autodet.gw.stats.lh.dat lh.volume
autodet.gw.stats.rh.dat lh.volume.fsaverage.mgh
lh.area lh.volume.fsaverage.mris_preproc.log
lh.area.fsaverage.mgh lh.w-g.pct.mgh
lh.area.fsaverage.mris_preproc.log lh.white
lh.area.mid lh.white.preaparc
lh.area.pial lh.white.preaparc.H
lh.area.pial.fsaverage.mgh lh.white.preaparc.K
lh.area.pial.fsaverage.mris_preproc.log rh.area
lh.avg_curv rh.area.mid
lh.curv rh.area.pial
lh.curv.fsaverage.mgh rh.avg_curv
lh.curv.fsaverage.mris_preproc.log rh.curv
lh.curv.pial rh.curv.pial
lh.defect_borders rh.defect_borders
lh.defect_chull rh.defect_chull
lh.defect_labels rh.defect_labels
lh.defects.pointset rh.defects.pointset
lh.fsaverage.sphere.reg rh.fsaverage.sphere.reg
lh.inflated rh.inflated
lh.inflated.nofix rh.inflated.nofix
lh.jacobian_white rh.jacobian_white
lh.orig rh.orig
lh.orig.nofix rh.orig.nofix
lh.orig.premesh rh.orig.premesh
lh.pial rh.pial
lh.pial.T1 rh.pial.T1
lh.qsphere.nofix rh.qsphere.nofix
lh.smoothwm rh.smoothwm
lh.smoothwm.BE.crv rh.smoothwm.BE.crv
lh.smoothwm.C.crv rh.smoothwm.C.crv
lh.smoothwm.FI.crv rh.smoothwm.FI.crv
lh.smoothwm.H.crv rh.smoothwm.H.crv
lh.smoothwm.K1.crv rh.smoothwm.K1.crv
lh.smoothwm.K2.crv rh.smoothwm.K2.crv
lh.smoothwm.K.crv rh.smoothwm.K.crv
lh.smoothwm.nofix rh.smoothwm.nofix
lh.smoothwm.S.crv rh.smoothwm.S.crv
lh.sphere rh.sphere
lh.sphere.reg rh.sphere.reg
lh.sulc rh.sulc
lh.sulc.fsaverage.mgh rh.thickness
lh.sulc.fsaverage.mris_preproc.log rh.volume
lh.thickness rh.w-g.pct.mgh
lh.thickness.fsaverage.mgh rh.white
lh.thickness.fsaverage.mris_preproc.log rh.white.preaparc
Cheers, Mervin
________________________________
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 Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: 25 September 2023 21:43 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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The error says “ERROR: cannot find /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/lh.white.K”.
Can you send what your subject surf/ directory looks like - ‘ls -lt /media/mt/Expansion/Disk9/EDIS_751/ED751_SAG_MPRAGE_p2_NON-SSc.nii/surf/’?
Yujing
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 Mervin Tee Sent: Monday, September 25, 2023 9:39 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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HI Yujing,
Here's the log file you have requested. Do take note that I have followed a post to modify my recon-all from ln to cp. so, the commands might look different.
Cheers, Mervin
________________________________
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 Huang, Yujing <YHUANG43@MGH.HARVARD.EDUmailto:YHUANG43@MGH.HARVARD.EDU> Sent: 25 September 2023 20:49 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Can you send the recon-all.log?
Yujing
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 Mervin Tee Sent: Monday, September 25, 2023 2:53 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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Hi R,
Thanks for getting back, indeed a copy of those files doesn't help because just like what you have mentioned at some point a check failed and I could not proceed with the remaining steps of recon-all.
The command I pasted was obtain from the last line of the error log text file where it indicates where the step of which the error occurred. But the main error is mostly due to symlink on exFAT storage on linux.
Hence, the question here is if there is any solution that allows me to still work on external exFAT storage. As symlink doesn't seems to work on exFAT storage. As my data are bitlocked on an external storage, which doesn't allow me to change the format for the storage drive. So, I was hoping to look for a workaround that allows me to continue working on exFAT storage.
Cheers, Mervin
________________________________
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 fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> Sent: 25 September 2023 10:10 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> Subject: Re: [Freesurfer] Unable to complete all the steps of recon-all
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I don’t see an error message in what you posted below.
I would not assume changing soft links to actual copies of the same file (by a different name) will work, i.e., anything that makes a soft link may subsequently test for a soft link using the link name. That test will fail if the soft link has been replaced by an actual (duplicate) copy of the file. The expectation is when writing output e.g., during recon-all, that SUBJECTS_DIR points to a linux compatible file system that supports creating all the Linux file system file types (including soft links) and support all Linux file privileges.
-R.
On Sep 24, 2023, at 01:58, Mervin Tee <mervintee@nus.edu.sgmailto:mervintee@nus.edu.sg> wrote:
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Hi,
I'm trying to complete my recon-all command. I'm currently working on Ubuntu 22 and processing the images from an exFAT drive.
After digging a bit, I realised that symbolic links cannot be created on exFAT drives. I then came across another post that suggest to change all 'ln' to cp instead. While that works for the remaining steps. It started exiting with errors at this stage.
The stage where it stops #@# Qdec Cache preproc lh white.K fsaverage Wed Sep 13 15:40:33 +08 2023
The error that was in the error log. CMD mris_preproc --s ED751_SAG_MPRAGE_p2_NON-SSc.nii --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh
What should I do to resolve this issue?
Cheers,
Mervin
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you. _______________________________________________ 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://secure-web.cisco.com/1952PaFprNjjEP0Pe6xmY3n2niNs_AOx2nEKX6vd_KFri0A...https://secure-web.cisco.com/1jUjS9URn0TDrVDj7NxOU4XmrListW4OD7-S02Vkb56daEa0Z7UelKgPghQxnevk3-GVAB-vRAHy6zx4Lm2TqLQcPshiOD4DxEj_Jb3vyWYjsvUgIv0vqWowsYN4YHUgwznDoMiYfFxMdS3L6JmQK5mLQby-8GB9yciVNK5WRx709IQLVHyF1Emq8BQ5mhSH5F13D2tsBn75P0DI2IeXtorMOVIbG9_exm4ytSddOt6BWcZzc9UT9zeUzFSWZI0OLyG1Doir2tygVotul_gaiFQ/https%3A%2F%2Fddec1-0-en-ctp.trendmicro.com%3A443%2Fwis%2Fclicktime%2Fv1%2Fquery%3Furl%3Dhttps%253a%252f%252fsecure%252dweb.cisco.com%252f1WQa6%252dQYo7CLG38RjaZXEy1kHc1Qc5FCSUUVmVJ481k44DJOmWoYccUh%252dgc2SfqwmvltRplAcJm8JhEEjuECoMhx417JW%255fIazlotEkBq5MUt8TNVkes2lS9sRuDRahE1CoaxWZfgFpjuccMu1e%255f1SIdHZlrncDopVlLbEel5HiDH8PidT%252d3xaW0Y1r9uONMOzIR7Oq7CebNJyYYwHUKY56zQuGWUstESlD69Zizl2kZIaEfxLDmcxlAW9bQrMcuakIGyZ3JRxGlyRi4%255fH12AcfcMpjQgrJdcf3gtVmk3S5oQwYKGXpvkogxx%252dCvcQ0SdofRadGbWTiQ%255fei5qQ9eiEPg%252fhttps%25253A%25252F%25252Fddec1%252d0%252den%252dctp.trendmicro.com%25253A443%25252Fwis%25252Fclicktime%25252Fv1%25252Fquery%25253Furl%25253Dhttps%2525253a%2525252f%2525252fsecure%2525252dweb.cisco.com%2525252f1FZd4cRvMJaVYQC3s%2525255f7vhvZrDnHhyJSq6ZpDFW5OppcooF4NkoM9HbMpY4AU4ozoi4oHj9ns12VNnlSNWhI9CipTbhqvYBM6y73mOGdB0J1h4wNa5wDv7SyUcOg6epDZ8NDdmWDu%2525255fc7dYv3bWLG9rHAJRvVpoagTWYrD1h3Mi7nCMeXbRad3iS7BuFoKOVJXY5D69ZATO8iN%2525252dEiM%2525255fQ2lb6AHFMSWd0lS1eetBXlDW2NaWwQ7ECDpdULruS%2525255fDSNTGaX5e3xwaLH7EKE9oq9OS3mTIwacwJ9tnTMW%2525252d1t5vMmLq00zy4sdDpvXXNXHdR9UHS%2525252fhttps%252525253A%252525252F%252525252Fddec1%2525252d0%2525252den%2525252dctp.trendmicro.com%252525253A443%252525252Fwis%252525252Fclicktime%252525252Fv1%252525252Fquery%252525253Furl%252525253Dhttps%25252525253a%25252525252f%25252525252fsecure%25252525252dweb.cisco.com%25252525252f1IO3u8TmP17OQfIG2beUfwjpisQihIq2KAEj37EkOmeU8dqNnRDA8Q0l1vRxZaWUktIPiOnVd9z2Vthsiq60E3E74ep0BvEFmJTh3eZLVpPAyct3E7CfGy8eTRVXScBQE6UZpQkblvNPUN69CKbO6AX54%25252525255f1uuvIK5G1unQnknF8y1zXgBKllrTG2KKsfDLrk7XA9mR7SUz9vjrbY2ARnuqF3jPZo%25252525255fMvWEABNXgA%25252525255fG34Y6iaWCvJlhkB%25252525255f60eprJBBWyD5s2Q2Pc6Q%25252525255fxf4q2ORhSdOJOiwyQ3av3pr2iTABSvR%25252525255fSGVkg3bLFyzuZn2UtpR9W4JMhw8lSLIga5t6P8bZQg%25252525252fhttps%2525252525253A%2525252525252F%2525252525252Fmail.nmr.mgh.harvard.edu%2525252525252Fmailman%2525252525252Flistinfo%2525252525252Ffreesurfer%2525252526umid%252525253Df432ea85%2525252da7ec%2525252d484a%2525252da559%2525252dff96c2b6828e%2525252526auth%252525253D8d3ccd473d52f326e51c0f75cb32c9541898e5d5%2525252daa05409f729694bd38c0f3b53f7ff1d9f61f682f%252526umid%25253D2f0588e1%252d6dc2%252d4e78%252d9321%252d45a3d6060b22%252526auth%25253D8d3ccd473d52f326e51c0f75cb32c9541898e5d5%252d22db823c25e89e111063f0cc7607c6685a7cbad9%26umid%3D748b1618-24f7-40a1-ba7b-91731af2704d%26auth%3D8d3ccd473d52f326e51c0f75cb32c9541898e5d5-653da3b7cf71945c70a092f53122dbce68dbf283
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Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
________________________________
Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.
freesurfer@nmr.mgh.harvard.edu
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fsbuild -
Huang, Yujing -
Mervin Tee