Dear Freesurfer experts,
I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows).
I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks!
I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything.
Thanks,
Yang
Hi Yang
hmmm, that is curious. I don't think those will have much if any impact on your results, but if you upload that subject I'll take a look. What version are you running?
cheers Bruce
On Tue, 4 Feb 2014, Qingyang Li wrote:
Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks!
I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything.
Thanks,
Yang
Hi Bruce,
Where should I upload the data to? I forgot to mention that the data that I am working with are from a longitudinal project. The image I sent is a base image generated from 2 time points. The Freesurfer I am running is "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0".
Thanks!
Yang
------ Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Yang
hmmm, that is curious. I don't think those will have much if any impact on your results, but if you upload that subject I'll take a look. What version are you running?
cheers Bruce
On Tue, 4 Feb 2014, Qingyang Li wrote:
Dear Freesurfer experts,
I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows).
I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks!
I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything.
Thanks,
Yang
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.
Hi Yang
if you go to the freesurfer wiki you'll find instructions on uploading data. Use the ftp site and tar and gzip the entire subject directory
cheers Bruce On Tue, 4 Feb 2014, Qingyang Li wrote:
Hi Bruce, Where should I upload the data to? I forgot to mention that the data that I am working with are from a longitudinal project. The image I sent is a base image generated from 2 time points. The Freesurfer I am running is "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0".
Thanks!
Yang
Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Yang
hmmm, that is curious. I don't think those will have much if any impact on your results, but if you upload that subject I'll take a look. What version are you running? cheers Bruce On Tue, 4 Feb 2014, Qingyang Li wrote: Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks! I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything. Thanks, YangThe 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.
Hi Bruce,
The data is now on the ftp. The path to the file is "/transfer/incoming/003.tgz".
Thanks,
Yang
------ Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:45 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Yang
if you go to the freesurfer wiki you'll find instructions on uploading data. Use the ftp site and tar and gzip the entire subject directory
cheers Bruce On Tue, 4 Feb 2014, Qingyang Li wrote:
Hi Bruce,
Where should I upload the data to? I forgot to mention that the data that I am working with are from a longitudinal project. The image I sent is a base image generated from 2 time points. The Freesurfer I am running is "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0".
Thanks!
Yang
Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Yang
hmmm, that is curious. I don't think those will have much if any impact on your results, but if you upload that subject I'll take a look. What version are you running? cheers Bruce On Tue, 4 Feb 2014, Qingyang Li wrote: Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks! I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything. Thanks, YangThe 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.
Hi Yang
the problem is that the white matter of the parahippocampal gyrus is so dark that the surface deforms into hippocampus, which creates little holes in our estimate of what is cortex. You can see this by loading the lh.cortex.label into tksurfer. You could fix it by filling in the holes in the cortex label and rerunning the cortical parcellation. Or you could try editing the brain.finalsurfs.mgz I guess to brighten up those voxels, but they are *very* dark - barely any contrast there at all with the GM.
Depending on what you are planning to do with this data I would guess it's not something to worry about at all. It just two very small holes that won't appreciaably change any statistics. cheers Bruce
On Tue, 4 Feb 2014, Qingyang Li wrote:
Hi Bruce, The data is now on the ftp. The path to the file is "/transfer/incoming/003.tgz".
Thanks,
Yang
Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:45 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Yang
if you go to the freesurfer wiki you'll find instructions on uploading data. Use the ftp site and tar and gzip the entire subject directory cheers Bruce On Tue, 4 Feb 2014, Qingyang Li wrote: Hi Bruce, Where should I upload the data to? I forgot to mention that the data that I am working with are from a longitudinal project. The image I sent is a base image generated from 2 time points. The Freesurfer I am running is "freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0". Thanks! Yang ------ Qingyang Li Balance and focus. On Tue, Feb 4, 2014 at 8:30 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Yang hmmm, that is curious. I don't think those will have much if any impact on your results, but if you upload that subject I'll take a look. What version are you running? cheers Bruce On Tue, 4 Feb 2014, Qingyang Li wrote: Dear Freesurfer experts, I was looking at the results of my data when I found that there were some black spots in my parcellation results (Please see the attached screenshot, the black spots were indicated by arrows). I did not see any hole or other errors in the surfaces generated for this subject. I hope you can help me with why the black spots were there? is it a big deal or something that I can ignore? If they need to be fixed, what should I do? Thanks! I am sorry if this question has been posted here. I really tried to find the answer by myself but I did not find anything. Thanks, Yang 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Qingyang Li