Thank you Bruce and Khoa for the suggestions. We used control points to add wm regions and this corrected the pial surface as you mentioned. We also filled in the topological defects in the wm.mgz file (using add voxels tool) and ran autorecon2. However, we noticed that the new wm segment now has black voxels (~1 each) that were not present in the previous segment. Do you have any ideas about what may be the cause? How significant are these one voxel defects?
Also, is there a suggested order for running autorecon2? Based on the responses, it appears that we should run autorecon2 for white matter segment and control points simultaneously and later regenerate the pial surface. Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: vy_d...@rush.edu ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, September 16, 2011 7:38 AM To: k...@nmr.mgh.harvard.edu Cc: Jing Ming; s...@nmr.mgh.harvard.edu; Jennifer G Goldman; Vy Dinh; Freesurfer Subject: Re: [Freesurfer] manual editting problem p.s. you also have topological defects there, which you can tell as the orig (green) surface doesn't follow the voxels in the wm.mgz. The interventions Khoa suggests should help this as well. If you are missing that much wm you probably want to use control points. cheers Bruce On Thu, 15 Sep 2011, k...@nmr.mgh.harvard.edu wrote: > Hi Jing, > > You have some white matter voxels missing in the wm.mgz for the rh. You > can add some wm to that volume using the edit tool or you can also try > control points. If you are adding wm, make sure you select the aux volume > on the brush info toolbox. Fill in wm voxels for all slices. Control > points would help with extending the pial surf on the lh. > > -Khoa > >> >> Hi Bruce and Sita: >> >> Thanks for your relay. And Here are the images. >> >> Jing >> >> >> >> From: Jing Ming [mj_com...@hotmail.com] >> >> Sent: Thursday, September 15, 2011 7:31 PM >> >> To: Vy Dinh >> >> Subject: FW: [Freesurfer] manual editting problem >> >> >> >> >> >> >> >> >> >> >>> CC: mj_com...@hotmail.com; jennifer_g_gold...@rush.edu; vyd...@rush.edu; >>> freesurfer@nmr.mgh.harvard.edu >> >>> From: fis...@nmr.mgh.harvard.edu >> >>> Subject: Re: [Freesurfer] manual editting problem >> >>> Date: Thu, 15 Sep 2011 20:07:41 -0400 >> >>> To: s...@nmr.mgh.harvard.edu >> >>> >> >>> Can you send an image? >> >>> >> >>> >> >>> >> >>> On Sep 15, 2011, at 6:38 PM, Sita Kakunoori <s...@nmr.mgh.harvard.edu> >>> wrote: >> >>> >> >>>> >> >>>> How does the wm.mgz look. Correcting the white surface will correct >>> the >> >>>> pial surface as well. >> >>>> >> >>>> Sita. >> >>>> >> >>>> >> >>>> On Thu, 15 Sep 2011, Jing Ming wrote: >> >>>> >> >>>>> >> >>>>> Hi Surfers: >> >>>>> We have been coming >> >>>>> across several gray matter regions that are not included within the >>> pial >> >>>>> surface (red line) when it should be (e.g., very anterior parts of >>> the >> >>>>> temporal lobe). From my understanding of similar posts on the forum, >>> it >> >>>>> seems that there isn't a way to add this region to the pial surface >>> so >> >>>>> that the missing brain matter is included. We have tried using the >>> clone >> >>>>> tool to fill in this region, as per the tutorial and have >>> experimented >> >>>>> with this tool using the tutorial data. I followed the steps in the >> >>>>> tutorial but could not observe any changes when the middle button was >> >>>>> selected. Does anyone have any ideas on how to troubleshoot this >> >>>>> issue? Can someone please explain to me why this is not possible? >>> Also >> >>>>> how does Freesurfer determine what regions to include within the pial >> >>>>> surface? If there is a way that has been developed recently, please >> >>>>> enlighten me. >> >>>>> >> >>>>> -Jing >> >>>> _______________________________________________ >> >>>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
