Re: [Freesurfer] diluting a mask using inflated brain
Jodie, you might also look into using the white matter parcellation. That would allow you to select the WM from a particular gyrus. doug On 01/29/2013 03:31 PM, Jodie Davies-Thompson wrote: > > Dear Freesurfer users and experts, > > We are attempting to grow a mask that we have created in FSL, to > expand it into white matter. > > At first, we tried this in FSL using the dilM command which dilated > the size of the mask by n voxels. We then multiplied this by a > segmented white matter mask (again, created in FSL) so only the white > matter voxels were included. However, a problem with this method, is > that if a mask is over a gyri (as most of our masks are), then > diluting the mask in a non-inflated brain causes some voxels from an > adjacent gyri to be included. > > What we would like to be able to do, is to dilute the mask using the > inflated white matter brain created by Freesurfer, and then to take > this back into FSL space; thereby, allowing us to create a mask of > which includes the true surrounding white matter rather than white > matter from adjacent gyri. > > Hope this makes sense!? Does anyone know how to do this or could point > us in the right direction? > > Cheers, > > Jodie > > - > > --- > > Jodie Davies-Thompson, Postdoctoral Fellow > > Department of Ophthalmology & Visual Sciences > > UBC/VGH Eye Care Centre > > 2550 Willow Street > > Vancouver, BC, V5Z 3N9 > > Canada > > Tel: 604-875-4111 ext 69003 > > > > ___ > 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: 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 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.
Re: [Freesurfer] diluting a mask using inflated brain
Hi Jodie you can do this on the surface, then project the resulting label 1mm into the white matter if I understand what you want correctly. You might also check out the wmparc.mgz and see if it already does what you want. cheers Bruce On Tue, 29 Jan 2013, Jodie Davies-Thompson wrote: Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003 ___ 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] diluting a mask using inflated brain
Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111 ext 69003 ___ 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.
