Hello, I have tried fixing the image using the topical defects page. However, because it uses recon-edit the affected area does not seem to be recognized as white matter. Is it okay to do free editing for the same results, or is there something else that I should try for implementation? Thank you for the help,
Nicholas Goh On Mon, Oct 23, 2017 at 4:10 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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_freeview > > > 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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* <ngo...@gmail.com > >>> <mailto:ngo...@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 > >>> <ngo...@gmail.com <mailto:ngo...@gmail.com>> wrote: > >>> > >>> Ping, is this okay to do? I Think it is but wanted to > >>> check before sending > >>> ---------- Forwarded message ---------- > >>> From: *Bruce Fischl* <fis...@nmr.mgh.harvard.edu > >>> <mailto:fis...@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 > >>> <fk...@medschl.cam.ac.uk > >>> <mailto:fk...@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 > >>> (ngo...@gmail.com <mailto:ngo...@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 > >>> <fis...@nmr.mgh.harvard.edu > >>> <mailto:fis...@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> . 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> > >>> > >>> > >>> 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:freesur...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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.
