Hi Vy, You shouldn't worry about those black voxels as long as the surfaces are ok. As for the command, you only need to run:
recon-all -autorecon2 -autorecon3 -subjid anon -autorecon2-wm and -autorecon2-pial are both downstream from -autorecon2 so you do not need to include those flags. -autorecon2-cp is the same as -autorecon2 so you can start from the beginning of -autorecon2 whenever you use control points. For pial surf editing, you only need to make these edits when the pial surf includes remaining dura/skull. If you want to extend pial surf to include more gm, you need to make edits to the wm.mgz or add control points. If your subject has improved after the control points and wm edits but is not perfect, you can try adding more control points or look for more topological defects to fix. Hope that helps, -Khoa On Wed, 21 Sep 2011, Vy Dinh wrote: > Hi Khoa, Thanks for the fast reply! I've attached the pictures of the wm.mgz before and after we ran autorecon2 and autorecon3. Initially, we made corrections to wm edits, added control points, and corrected pial surface. We used the command: recon-all -autorecon2-wm -autorecon2-pial -autorecon2-cp -autorecon3 -subjid anon The control points over extended the pial surface in some regions, so we conclude that it's better to correct the pial surface after we had regenerated the surfaces for the control points. 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: Khoa Nguyen [k...@nmr.mgh.harvard.edu] Sent: Wednesday, September 21, 2011 3:58 PM To: Vy Dinh Cc: Bruce Fischl; Jing Ming; s...@nmr.mgh.harvard.edu; Jennifer G Goldman; Freesurfer Subject: RE: [Freesurfer] manual editting problem Hi, Do you mind sending a snapshot so I see what the black voxels look like? If you add control points and make wm edits and pial edits, running -autorecon2 -autorecon3 should take care of everything. If you're only making wm and pial edits, then run -autorecon2-wm -autorecon3. If only pial edits, then run -autorecon-pial. Here's a wiki page of all the recon steps. On there you can also find the OtherUsefulFlags page with different flags you can use when running your recons. http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable -Khoa On Wed, 21 Sep 2011, Vy Dinh wrote: > 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
