[Freesurfer] Single Hemisphere Option Availability for Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal)

[Park, James]

External Email - Use Caution

Dear Freesurfer team,

Thank you so much for your support for this software thus far.

As we were considering using the module for segmentation of hippocampal 
subfields and nuclei of the amygdala (cross-sectional and longitudinal), we 
came across an interesting scenario:
Due to certain conditions for some subjects we seek to analyze, we would like 
to only run this module of freesurfer on one hemisphere.
I understand that recon -all has this option (-hemi ?h) but found that there 
was no documentation regarding single hemisphere segmentation of the 
Hippocampus / Amygdala.

Could you let us know if there are any hidden options that enable single 
hemisphere processing or workflows that allow for this?

Thank you so much for your help as always.

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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed}

[Park, James]

External Email - Use Caution

Dear Freesurfer Team,

Hello, my name is James Park and I have recently been trying to utilize 
Freesurfer on a new Windows Computer.

I was able follow the instructions provided on : 
https://secure-web.cisco.com/1eXouftPDgg37AuJADlljMENUWBEUfGROCh_5ifJ-wvqNhQPRfgpHWXJB0SkxVJsoLoBoMaMOW-JIUWuRvlPsLVfRR3D6vJxKSTB8me_P6MfSy2wa7QdKRD2dN9wYwmNcJpQTyK1pIc_jm6pe-D_nM6G7LkSa6DBhjpVTULK58OVW-zUor9RC6G3dqGxU6s-Nxk2sA8fnPhcfAWRhcvbOSZ-IQIK8Jff_nU_YgrA5zgv5jf4bBhCUaaBDb4JpSxHeO0IHaPdBbKIiLNGae1DnTA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FVM_67_win
 but unfortunately was unable to log into the desktop of the virtual machine 
because it requires a password for the “developer” account.

I noticed in previous mailing archives this password was sent privately – could 
I also receive this password by chance?

Thank you for your help in advance.

Sincerely,
James Park
email: james.kunwoo.p...@emory.edu




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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Park, James]

External Email - Use Caution

Thank you!

This has been super helpful.

Sincerely,
James Park

From: freesurfer-boun...@nmr.mgh.harvard.edu 

Date: Tuesday, October 27, 2020 at 2:21 PM
To: Freesurfer support list 
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:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Tuesday, October 27, 2020 at 12:12 PM
To: FS Help 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list 
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:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Park, James]

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Hoopes, Andrew 

Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list 
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:  on behalf of "Park, James" 

Reply-To: FS Help 
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help 
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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [External] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

[Park, James]

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-boun...@nmr.mgh.harvard.edu 

Date: Monday, October 26, 2020 at 3:01 PM
To: 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.p...@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).
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Park, James]

External Email - Use Caution

Dear Freesurfer Team,

Thank you for this update.

How can I replace the current recon-all script with this new script?
Do I just replace the recon-all script located in the “bin” folder with this 
new script?

Additionally, I was wondering if you knew when these changes might formally be 
incorporated in a later version of freesurfer.

Thank you again for your help in advance.

Sincerely,
James Park

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, September 8, 2020 at 6:42 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for 
Freesurfer, error in the cortical ribbon mask stage during recon-all


Try using this version of recon-all
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel

On 9/8/2020 12:09 PM, Park, James wrote:

External Email - Use Caution
Hello,

Thank you for such a prompt response.

This has happened consistently and across multiple mac laptops that we utilize 
in our laboratory.

Below is the freesurfer version that we are utilizing as noted in the 
build-stamp.txt file:
freesurfer-darwin-macOS-7.1.1-20200811-8b40551

That would be great thank you so much.

Sincerely,
James Park

From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, September 8, 2020 at 12:06 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] Troubleshooting -parallel flag for 
Freesurfer, error in the cortical ribbon mask stage during recon-all

The issue with the ribbon is something we recently became aware of. does it 
happen consistently for you? I can send you a recon-all that will fix this for 
you, just tell me which version you are running.


On 9/8/2020 11:49 AM, Park, James wrote:

        External Email - Use Caution


Sincerely,
James Park

From: "Park, James" 
<mailto:james.kunwoo.p...@emory.edu>
Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical 
ribbon mask stage during recon-all

Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze T1 MRI data 
and ran into an error specifically when utilizing the -parallel flag.

We specifically ran into errors at the cortical ribbon mask stage during the 
code we ran (shown below with some parts of the paths removed).

recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd 
“…/freesurfer_output" -all -parallel

When the same code was run without the -parallel flag, the recon-all line ran 
successfully.

This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

The recon-all.log file has been attached here as a reference.

Thank you for your help in advance.

Sincerely,
James Park
Willie Lab, Dpt. of Neurosurgery, Emory



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 mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Park, James]

External Email - Use Caution

Hello,

Thank you for such a prompt response.

This has happened consistently and across multiple mac laptops that we utilize 
in our laboratory.

Below is the freesurfer version that we are utilizing as noted in the 
build-stamp.txt file:
freesurfer-darwin-macOS-7.1.1-20200811-8b40551

That would be great thank you so much.

Sincerely,
James Park

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, September 8, 2020 at 12:06 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [External] Re: [Freesurfer] Troubleshooting -parallel flag for 
Freesurfer, error in the cortical ribbon mask stage during recon-all

The issue with the ribbon is something we recently became aware of. does it 
happen consistently for you? I can send you a recon-all that will fix this for 
you, just tell me which version you are running.

On 9/8/2020 11:49 AM, Park, James wrote:

External Email - Use Caution


Sincerely,
James Park

From: "Park, James" 
<mailto:james.kunwoo.p...@emory.edu>
Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical 
ribbon mask stage during recon-all

Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze T1 MRI data 
and ran into an error specifically when utilizing the -parallel flag.

We specifically ran into errors at the cortical ribbon mask stage during the 
code we ran (shown below with some parts of the paths removed).

recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd 
“…/freesurfer_output" -all -parallel

When the same code was run without the -parallel flag, the recon-all line ran 
successfully.

This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

The recon-all.log file has been attached here as a reference.

Thank you for your help in advance.

Sincerely,
James Park
Willie Lab, Dpt. of Neurosurgery, Emory



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 mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Park, James]

External Email - Use Caution



Sincerely,
James Park

From: "Park, James" 
Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical 
ribbon mask stage during recon-all

Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze T1 MRI data 
and ran into an error specifically when utilizing the -parallel flag.

We specifically ran into errors at the cortical ribbon mask stage during the 
code we ran (shown below with some parts of the paths removed).

recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd 
“…/freesurfer_output" -all -parallel

When the same code was run without the -parallel flag, the recon-all line ran 
successfully.

This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

The recon-all.log file has been attached here as a reference.

Thank you for your help in advance.

Sincerely,
James Park
Willie Lab, Dpt. of Neurosurgery, Emory



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).


recon-all-status.log
Description: recon-all-status.log
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer