Thanks Lee, I am testing it right now. Just to be sure, it means that a value of 1 in the wm.mgz volume would be treated differently from a value of 0? I did not touch the wm.mgz volume in those regions because I didn't see anything to delete, but it is interesting to know that even if the sulci were already with a value of 0 in the WM.mgz, it can be helpful to change it to 1. Thanks a lot for the tips (and also the visualization tip, super helpful :-) Celine
> Hi Celine, > > I took a look at you data, and made some edits to the wm that help to push > out the surfaces to the bottom of the sulci. I attached screenshots of > the same slices you sent before, with the original white and pial surfaces > in green and blue, and the ones created after editing in yellow and red. > Below are some instructions on how to make these edits. > > First, select the wm volume and change the color map to Heat on the panel > on the lower left. Set the opacity to ~0.15-0.25 so you can see the > brainmask behind it. Then, lower the Mid to zero (where my pointer is in > wm_edit_1.png; you can keep the other values at their defaults). By doing > this, everything that you erase using Recon Edit will show up in red so > that it is easy to see. Next, erase a line at the start of the sulcus > where you want to push out the surface (wm_edit_2.png), then select the > fill tool and hold shift and click inside the sulcus to erase the whole > section (wm_edit_3.png). Do this for a few slices around each location > that needs to be pushed out so that it has more effect, then save the wm > volume and rerun recon-all. > > Hope this helps, and let me know if you have any more questions. > > Best, > Lee > > On Wed, 21 Jan 2015, Celine Louapre wrote: > >> Hi everyone >> I don't know if someone had the chance to look at the data we uploaded >> for advice to edit the recons (see below). >> Thank you so much >> Celine >> >> On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote: >>> Thanks Bruce >>> The aseg is correct, no ventricule labeled there (I was used to that) >>> that I could see. I couldn't find the topological defect indeed, and >>> what is strange if that the wrong surface on the right hemisphere were >>> correct after autorecon2 but incorrect after autorecon3. The problem on >>> the left hemisphere was already present after autorecon2. >>> >>> I have uploaded the recon directory there: >>> https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/32464/1/2115a25100be43906c26359fbbd1ed08 >>> >>> Thank you again :-) >>> Celine >>> >>> On Fri, 2015-01-16 at 11:03 -0500, Bruce Fischl wrote: >>>> Hi Celine >>>> >>>> hard to tell from the slices. Are there voxels labeled ventricle >>>> there? >>>> If so, you need to correct the aseg. If not, it's probably a >>>> topological >>>> defect that is fixed incorrectly. If you upload the subject we'll take >>>> a >>>> look >>>> Bruce >>>> On Fri, 16 Jan 2015, Celine Louapre wrote: >>>> >>>>> Sorry forgot the attachement :-) >>>>> >>>>>> Hi Freesurfer team >>>>>> We have been struggling with editing recon for one patient, see the >>>>>> 2 >>>>>> slices attached. The problem is that the surface don't go all the >>>>>> way up >>>>>> to the bottom of the sulci. I had this some times before but usually >>>>>> managed to fix it with editing the wm and the aseg, but this time I >>>>>> couldn't have it work correctly. Would you have a clue to help me on >>>>>> that? >>>>>> I can put the data in some folders if you want to take a look at the >>>>>> entire volumes. >>>>>> Thanks for your help >>>>>> Celine >>>>>> >>>>>> -- >>>>>> Celine Louapre, MD-PhD >>>>>> Research Fellow at Massachusetts General Hospital >>>>>> Department of Radiology, MGH >>>>>> >>>>>> Building 149, Room 2301 >>>>>> 13th Street >>>>>> Charlestown, MA 02129 >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ 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.
