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