Hi Mehul, Mehul Sampat wrote: > Thanks Doug. > > Using mri_label2vol is a good idea and I will use this approach. > Now to create the individual binary masks I just need to use > mri_label2vol, followed by mri_binarize: > > For example: > > a. mri_label2vol --seg aparc+aseg.mgz --regheader rawavg.mgz --o > aparc+aseg-in-rawavg.mgz --temp aparc+aseg.mgz The template here should be rawavg.mgz, I think. > b. mri_binarize --i aparc+aseg-in-rawavg.mgz --match 1022 --o > lh-postcentral.nii > > Also, when I looked at the help, I first thought I could do the same > thing with mri_annotation2label followed by mri_label2vol . > > for example: > > a. mri_annotation2label --subject bert --hemi lh --annotation aparc > --outdir labels > b. mri_label2vol --label ../labels/lh.postcentral.label --regheader > rawavg.mgz --o lh-postcentral.nii --temp aparc+aseg.mgz Again, use rawavg.mgz as the temp. Also you should be able to use mri_label2vol directly on the annotation (with --annot).
doug > > But when I checks the results, (from using mri_annotation2label > followed by mri_label2vol), the individual binary mask looks incorrect > Did I make an error in the second approach ? > > Thanks > Mehul > > > > > On Tue, Jul 13, 2010 at 2:41 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > I think either should work, though I am more comfortable with > mri_vol2vol. Depending on what you are doing you might want to use > mri_label2vol. This can convert the aseg.mgz directly to the > native anatomical space. The main difference is that it will > resolve boundary voxels by voting. With your method, you will have > some voxels that will be in more than one label, which may or may > not be a problem depending on what you are doing. > > doug > > Mehul Sampat wrote: > > Hi Folks, > > I would like to create binary masks for any given structure in > aseg.mgz and aparc+aseg.mgz. > I would then also like to map the masks back to native space. > > I think, I should use mri_binarize followed by mri_convert as > shown in the two examples below: > > Example 1: > a. mri_binarize --i mri/aseg.mgz --match 10 --o > deep-gm-rois/lh-thalamus.mgz > b. mri_convert -rl mri/orig/001.mgz -rt nearest > deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii > > Example 2: > a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o > ctx-gm-rois/lh-postcentral.mgz > b. mri_convert -rl mri/orig/001.mgz -rt nearest > ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii > > Ques 1: Is the best approach for this task ? > > I noticed in the FAQ that mri_vol2vol is recommended for > conversion from freesurfer space to anantomical space. > > Ques 2: Is it better to use mri_vol2vol than mri_convert with > the reslice option ? > Thanks > Mehul > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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 _______________________________________________ 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.
