External Email - Use Caution
Hello,
My name is James Park, and I had a question regarding some issues with Freesurfer.
We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others. Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).
I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location. I was wondering if there is any workaround for this issue?
This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
Thank you for your help in advance.
Sincerely, James Park Research Specialist Dpt. of Neurosurgery, Emory james.kunwoo.park@emory.edumailto:james.kunwoo.park@emory.edu 732-589-4215
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
External Email - Use Caution
Hello,
Sorry for the rapid follow up email, I just noticed I left some personal contact information on the previous email.
Could you please remove my signature from the archives?
Thank you so much.
Sincerely, James Park
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Date: Monday, October 26, 2020 at 3:01 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution Hello,
My name is James Park, and I had a question regarding some issues with Freesurfer.
We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others. Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).
I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location. I was wondering if there is any workaround for this issue?
This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
Thank you for your help in advance.
Sincerely, James Park Research Specialist Dpt. of Neurosurgery, Emory james.kunwoo.park@emory.edumailto:james.kunwoo.park@emory.edu 732-589-4215
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Hi James,
It sounds like your target filesystem does not support symlinks? The answer to your question depends on how you are actually copying data, and you should probably contact your IT about this, but if you’re using rsync to move recons, you can supply the --copy-links flag to transform symlinks into referent file/dir.
best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Park, James" james.kunwoo.park@emory.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, October 26, 2020 at 3:03 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution Hello,
My name is James Park, and I had a question regarding some issues with Freesurfer.
We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others. Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).
I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location. I was wondering if there is any workaround for this issue?
This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
Thank you for your help in advance.
Sincerely, James Park ________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
External Email - Use Caution
Hi Andrew,
Thank you so much for your prompt response.
Our IT department was unfortunately a bit unfamiliar with these types of files.
We were not using rsync to move our files but instead just copying the files over through a file explorer.
Could you please point me in the right direction as to where I could access more information on rsync or moving data to a different location?
That would be super helpful!
Thank you again for your help.
Sincerely,
James Park
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Monday, October 26, 2020 7:16 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
Hi James,
It sounds like your target filesystem does not support symlinks? The answer to your question depends on how you are actually copying data, and you should probably contact your IT about this, but if you’re using rsync to move recons, you can supply the --copy-links flag to transform symlinks into referent file/dir.
best,
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Park, James" james.kunwoo.park@emory.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, October 26, 2020 at 3:03 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution
Hello,
My name is James Park, and I had a question regarding some issues with Freesurfer.
We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others.
Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).
I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location.
I was wondering if there is any workaround for this issue?
This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
Thank you for your help in advance.
Sincerely,
James Park
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
Hi James,
Rsync is a very common unix command for syncing/copying across filesystems. There’s plenty of information about it online, and you can access the help text through `man rysnc`. This might be useful https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Park, James" james.kunwoo.park@emory.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Tuesday, October 27, 2020 at 12:12 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution Hi Andrew,
Thank you so much for your prompt response.
Our IT department was unfortunately a bit unfamiliar with these types of files.
We were not using rsync to move our files but instead just copying the files over through a file explorer.
Could you please point me in the right direction as to where I could access more information on rsync or moving data to a different location?
That would be super helpful!
Thank you again for your help.
Sincerely,
James Park
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Monday, October 26, 2020 7:16 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
Hi James,
It sounds like your target filesystem does not support symlinks? The answer to your question depends on how you are actually copying data, and you should probably contact your IT about this, but if you’re using rsync to move recons, you can supply the --copy-links flag to transform symlinks into referent file/dir.
best,
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Park, James" james.kunwoo.park@emory.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, October 26, 2020 at 3:03 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution
Hello,
My name is James Park, and I had a question regarding some issues with Freesurfer.
We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others.
Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).
I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location.
I was wondering if there is any workaround for this issue?
This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
Thank you for your help in advance.
Sincerely,
James Park
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
External Email - Use Caution
Thank you!
This has been super helpful.
Sincerely, James Park
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Date: Tuesday, October 27, 2020 at 2:21 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location Hi James,
Rsync is a very common unix command for syncing/copying across filesystems. There’s plenty of information about it online, and you can access the help text through `man rysnc`. This might be useful https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Park, James" james.kunwoo.park@emory.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Tuesday, October 27, 2020 at 12:12 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution Hi Andrew,
Thank you so much for your prompt response.
Our IT department was unfortunately a bit unfamiliar with these types of files.
We were not using rsync to move our files but instead just copying the files over through a file explorer.
Could you please point me in the right direction as to where I could access more information on rsync or moving data to a different location?
That would be super helpful!
Thank you again for your help.
Sincerely,
James Park
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Monday, October 26, 2020 7:16 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
Hi James,
It sounds like your target filesystem does not support symlinks? The answer to your question depends on how you are actually copying data, and you should probably contact your IT about this, but if you’re using rsync to move recons, you can supply the --copy-links flag to transform symlinks into referent file/dir.
best,
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Park, James" james.kunwoo.park@emory.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, October 26, 2020 at 3:03 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location
External Email - Use Caution
Hello,
My name is James Park, and I had a question regarding some issues with Freesurfer.
We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others.
Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).
I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location.
I was wondering if there is any workaround for this issue?
This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.
Thank you for your help in advance.
Sincerely,
James Park
________________________________
This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.
If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Park, James