23 Oct
2017
23 Oct
'17
4:10 p.m.
I think you have an incorrectly fixed defect at that location. Follow the instructions on fixing defects on our wiki. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...
On 10/23/2017 09:18 AM, Nicholas Goh wrote:
Sorry for the delay, I was hoping to get some input from another on why my numbers seemed off. I have attached a screenshot which I believe has an image of an example which needs to be fixed, along with the coordinates. Please let me know if you need anything else,
Nicholas Goh
On Mon, Oct 16, 2017 at 1:08 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't know what coordinates those are. Can you give indices? indices are non-neg On 10/16/17 12:59 PM, Nicholas Goh wrote:An example of the aparc+aseg not covering all that it needs to can be found around [-7, 114, 133] On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: what is the index (ie, col, row, slice) where you are seeing a problem? On 10/16/17 11:44 AM, Nicholas Goh wrote: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> . 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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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <http://www.partners.org/complianceline> . 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