Hi, I was following the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview after being told that the images linked earlier in this email thread were unable to add white matter (by adding control points) because of a topological defect. I opened the files and used the recon edit to add voxels, since recon edit was suggested on the wiki, and then ran recon-all -autorecon2-wm -autorecon3 -subjid XXXX However, the added voxels were being seen as part of the region assigned a value of 255 (default recon edit value) and not as white matter. Should I try to add voxels in a different brush value corresponding to the white matter, or is there some other way to correct this value? Thank you,
Nicholas Goh On Tue, Oct 31, 2017 at 11:27 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Nicholas > > can you tell us exactly what you did. What volume did you edit? What > command did you run? That kind of thing > > cheers > Bruce > > > > On Tue, 31 Oct 2017, Nicholas Goh wrote: > > Hello, >> I tried to correct a topological defect as described on the wiki but it >> did not produce the proper value. Because >> the wiki said to use recon-edit, any additions made were given a value of >> 255 and not seen as possible white >> matter. Would it cause a problem if I were to use free editing and >> changing the brush value to the correct one? >> or is there another way to address this issue? >> Thanks, >> >> Nicholas Goh >> >> On Wed, Oct 25, 2017 at 9:32 AM, Nicholas Goh <ngo...@gmail.com> wrote: >> 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/Topolog >> icalDefect_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.har >> vard.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. > >
_______________________________________________ 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.
