Hi,
I am not sure if this email got lost in the process or is still awaiting approval, but I was asked to tar and gzip the images that I was having no luck with fixing the white matter for. Any help would be appreciated. Thank you,
Nicholas Goh ---------- Forwarded message ---------- From: Nicholas Goh ngoh95@gmail.com Date: Mon, Oct 2, 2017 at 12:33 PM Subject: Re: [Freesurfer] Adding control points to aparc+aseg To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
I have still been having trouble with fixing the white matter of the aparc+aseg.mgz file for a subject. I have tried using
recon-all -autorecon2-cp -autorecon3 -subjid XXXX recon-all -autorecon2-wm -subjid XXXX recon-all -autorecon2-wm -autorecon3 -subjid XXXX
None of these have solved the issue, and I was hoping for help in finding a way to fix this? There are other more extreme examples, but this one seems to have an error at [-7, 114, 133] Thank you for the help,
Nicholas Goh
On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh ngoh95@gmail.com wrote:
Ping, is this okay to do? I Think it is but wanted to check before sending ---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: Thu, Sep 28, 2017 at 5:23 PM Subject: Re: [Freesurfer] Adding control points to aparc+aseg To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi Nicholas
why don't you tar, gzip and upload your subject and we will take a look. Make sure to tell us the coordinates of where you are trying to fix things
cheers Bruce
On Thu, 28 Sep 2017, Nicholas Goh wrote:
I am still having trouble with getting the aparc+aseg to recognize sections
that should be white matter as such. Using the control points paired withrecon-all -autorecon2-cp -autorecon3 -subjid XXXX
did not work, after 4 or 5 attempts with different control points, and using recon-all -autorecon2-wm -s XXXX also did not yield appreciable results. Is there anything else that I might be able to try to fix this? Thank you for all the help,
Nicholas Goh
On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak fkm24@medschl.cam.ac.uk wrote: Hi Nicholas,
In such situations, I have learned that autorecon2-wm after adding WM voxels seems to work pretty well. Hope that helps.
Best Wishes, Elijah
On 27 September 2017 at 16:46:43, Nicholas Goh (ngoh95@gmail.com) wrote:
Bruce, Thank you for the response. Attempting to use this method has not produced results, and I am unsure how to proceed or if I had performed it improperly. I have attached an example of the control points being placed, if that helps any. Thank you,
Nicholas Goh
On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nicholas
yes, possibly, depending on why you are missing chunks. If the white matter in the regions you are missing has intensity values significantly < 110 then what you are doing should help. The control.dat file must be place in the subject/tmp dir for us to find it. cheers Bruce On Wed, 27 Sep 2017, Nicholas Goh wrote: I am attempting to fix the aparc+aseg.mgz file for an image, and wanted to check to see if I am doing it correctly.What I was doing which seemed to be ineffective was 1)create a new point set of control points labelled control.dat 2)place control points along what should be white matter 3)save point set 4)run recon-all -autorecon2-cp -autorecon3 -subjid XXXX Is this the correct way to go about fixing aparc+aseg files that are missing chunks of the brain? Is there a better way to go about this? Thanks for the help, Nicholas Goh _______________________________________________ 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.
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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.