Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi Mackenzie
have you used ftp before?
cheers Bruce
On Fri, 18 Aug 2017, Leavitt, Mackenzie wrote:
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
No I have not.
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, August 18, 2017 10:30 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
have you used ftp before?
cheers Bruce
On Fri, 18 Aug 2017, Leavitt, Mackenzie wrote:
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi Mackenzie, to use ftp, you can run this command to access the server:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a login, and you should use "anonymous" as your name. Use your email address when it prompts for a password. To upload a file (ex: file.tar.gz), run these two commands:
cd transfer/incoming put file.tar.gz
note: to compress a directory before uploading, you can use tar:
tar -zcvf output.tar.gz /path/to/dir
best, Andrew
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Leavitt, Mackenzie Leavitm@ccf.org Sent: Friday, August 18, 2017 1:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi,
No I have not.
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, August 18, 2017 10:30 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
have you used ftp before?
cheers Bruce
On Fri, 18 Aug 2017, Leavitt, Mackenzie wrote:
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Andrew!
The file is in the process of being uploaded now.
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Friday, August 18, 2017 11:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie, to use ftp, you can run this command to access the server:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a login, and you should use "anonymous" as your name. Use your email address when it prompts for a password. To upload a file (ex: file.tar.gz), run these two commands:
cd transfer/incoming put file.tar.gz
note: to compress a directory before uploading, you can use tar:
tar -zcvf output.tar.gz /path/to/dir
best, Andrew
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Leavitt, Mackenzie Leavitm@ccf.org Sent: Friday, August 18, 2017 1:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi,
No I have not.
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, August 18, 2017 10:30 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
have you used ftp before?
cheers Bruce
On Fri, 18 Aug 2017, Leavitt, Mackenzie wrote:
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list 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
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi Bruce,
Just uploaded the file to the ftp server. Let me know when you get a chance to look at it.
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, August 18, 2017 10:30 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
have you used ftp before?
cheers Bruce
On Fri, 18 Aug 2017, Leavitt, Mackenzie wrote:
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Hi,
I uploaded some data last week because our institution was having Contrast issues. I just wanted to send an e-mail to confirm that this information was received since I have not heard back yet.
Thank you for your assistance!
Best, Mackenzie Leavitt ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Leavitt, Mackenzie Leavitm@ccf.org Sent: Friday, August 18, 2017 11:42 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Bruce,
Just uploaded the file to the ftp server. Let me know when you get a chance to look at it.
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, August 18, 2017 10:30 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
have you used ftp before?
cheers Bruce
On Fri, 18 Aug 2017, Leavitt, Mackenzie wrote:
Hello Bruce,
How do I access the ftp site? When I attempt to follow the address the instructions give me, I am not able to find the site. Do you mind sharing the URL with me? I have the data ready to send you.
Thank you!
Best, Mackenzie ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Wednesday, August 16, 2017 7:04 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer Contrast Issues
Hi Mackenzie
if you upload a couple of subjects (their entire subject dir, tarred and gzipped) to our ftp site (directions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange)
I'll see what I can do
cheers Bruce
On Tue, 15 Aug 2017, Leavitt, Mackenzie wrote:
Hello,
Our institution is currently in the process of doing Quality Assurance on clinic data for the last 5 years. Naturally, we have large number of brains to go though.
Unfortunately, we keep noticing the same problem appear in the vast majority of the brains that we have looked at. The white matter is not being properly defined because it does not extend far enough into the cortex. Of the 750 brains in our current sample, 369 of them have this issue. It is not feasible to make individual edits on this many brains given the resources we have.
I have attached a PowerPoint containing an image of what the error looks like. In the PowerPoint, you will see that the white matter does not extend fully into the cortex, likely because the contrast is poor.
These images were acquired on a 3T MRI machine with an MPRAGE sequence. Given that it would not be feasible to do a manual edit on each of these brains to fill in the remaining WM, I wanted to reach out to see what can be done about this issue. Perhaps there is a more efficient way of fixing the problem with these images.
We greatly appreciate the assistance and support.
Best,
Mackenzie Leavitt
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
Freesurfer mailing list 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
===================================
Please consider the environment before printing this e-mail
Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Hoopes, Andrew -
Leavitt, Mackenzie