On 06/25/2013 12:12 PM, Colin Reveley wrote: > Doug - thanks that sounds well worth trying. > > the labels we have have arbitrary spatial resolution in the saggital > plane, and 1mm gaps between saggital slices. > > In general in this project we are using an isotropic resolution of 0.25mm. > > To generate surfaces in freesurfer I have to downsample to 0.35mm (to > fit into 256) > > in applying the procedure you suggest > > a) is it possible to use a volume with a dimension > 256? yes, you just have to have an accurate registration > b) is it possible to use a non-isotropic resolution? yes > > playing around with non-isotropic resolutions, projection fractions > and vote would yield different results. > > c) can mri_aparc2aseg output a volume > 256? I don't think so. But you can use mri_label2vol to map the 256 to your volume, though you will probably lose some resolution > > 0.35 isotropic will be ok. we'd prefer 0.25 if we can. > > best > > Colin > > > ---------- Forwarded message ---------- > From: Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > To: <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Cc: > Date: Sun, 23 Jun 2013 20:03:09 -0700 > Subject: Re: [Freesurfer] ribbon label volume mapping > > You could run mri_vol2surf at different projection fractions (and > using nearest neighbor interp). This will create a set of files, > one for each projection fraction. You can then run mri_concat with > the --vote option to get you the most frequently occurring label. > You could then use mris_seg2annot to create an annotation. > > If you want to go the other way, you will need to combine your > labels into an annotation (mris_label2annot), then convert that > into a volume with mri_aparc2aseg. > > doug > > > On 6/22/13 10:08 AM, Colin Reveley wrote: >> If one has a volume of integers, each representing a cortical area, >> can one map that to the surface as a set of labels, in a smart >> way that e.g. takes the mode of the voxels that lie on the vector >> between equivalent white and pial nodes (ie uses curvature and >> thickness information, tacitly or explicitly)? >> >> the labels are not exactly on the ribbon. There are many voxels >> outside the ribbon that are non zero. Like caudate etc. >> >> and some voxels that are within the ribbon but are zero because >> the label data is was/is non-isotropic originally (which is the >> problem we want to solve in fact). >> >> that would be great. >> >> Now let's say you already have labels on a mesh. >> >> can you generate a ribbon volume of labels, i.e. the opposite >> operation to what I enquire about above (opposite but not inverse >> operation)? >> >> This is work in rhesus. So my pipeline is very barebones indeed, >> really just >> >> mri_normalize >> ... >> mri_tesselate >> mri_inflate/smooth/sphere >> mris_fix_topology <-noaseg -noaprc> >> mris_make_surfaces <-naseg -noaparc> >> >> I only have access to what is generated by that sequence or what >> I can subsequently generate. >> I can generate a freesurfer like ribbon with mris_fill. >> >> My understanding of labels and data mapping in general in >> freesurfer is very poor. >> >> Maybe adapting one of your matlab scripts might be an idea, if >> there is not another way? >> >> many thanks, >> >> Colin, >> Sussex >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
