Hi Christopher see if mris_distance_transform does what you want.
cheers Bruce On Thu, 26 Jul 2012, Christopher Coello wrote: > Hi Bruce, > > Thanks for the reply. > I'm not really familiar with compiling C functions, I have been working all > the time with Matlab. Always worth to ask : do you have such set of C > functions in Matlab also ? > > Christopher > > On 25.07.2012 16:10, Bruce Fischl wrote: >> Hi Chris, >> >> sure, we can compute distance-to-surface transforms and such, but I >> don't think we have any pre-packaged binaries that will do what you >> want, just a set of C functions >> >> >> Bruce >> On Wed, 25 Jul 2012, Christopher Coello wrote: >> >>> Hi Bruce, >>> >>> Absolutely, the voxels I'm referring to are defined regarding their >>> distance to the cortical ribbon (let's say within 5 mm) rather than by >>> belonging to a specific tissue type. >>> Using a distance criteria from the ribbon surface and collect only >>> voxels within a certain distance (going outwards) could be one >>> solution. Is that possible with some functions in Freesurfer ? >>> >>> Chris >>> >>> On 25.07.2012 15:50, Bruce Fischl wrote: >>>> Hi Chris >>>> >>>> that's tough to do with only a T1 image as CSF and bone look the same. >>>> We don't have any ready-made tools for doing what you want, but you >>>> could probably get close with some rules. Sounds like the voxels you are >>>> referring to are CSF or dura given their proximity to brain >>>> cheers >>>> Bruce >>>> >>>> >>>> On Wed, 25 Jul 2012, Christopher Coello wrote: >>>> >>>>> Dear Freesurfer users, >>>>> >>>>> >>>>> I have been using the function mri_watershed with options -LABEL and >>>>> -atlas to segment into csf, scalp and skull. This option also gives a >>>>> segmentation of the gm and wm. All voxels of the head are assigned to >>>>> one of the labels. >>>>> >>>>> Nevertheless, the segmentation obtained in the file aseg.mgz of the >>>>> cortical ribbon is of much better quality the fast mri_watershed -LABEL >>>>> one. The problem is now if I use the csf obtained with mri_watershed >>>>> -LABEL together with the aseg.mgz gm segmentation, some voxels in the >>>>> border between cortical ribbon and csf are unassigned. >>>>> >>>>> My question is then : how could I generate a csf map like the one >>>>> obtained with mri_watershed -LABEL, but that is complementary of the >>>>> segmentation present in aseg.mgz of the cortical ribbon ? >>>>> >>>>> Thanks a lot in advance, >>>>> >>>>> Best, >>>>> >>>>> >>>> >>>> >>>> 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
