Hi Doug, That's very helpful, thank you! I have 2 follow-up questions though:
1. Is it possible to merge the cortical label (e.g. label 1001 ctx-lh-bankssts) with its corresponding label that extends into the WM (e.g. label 3001 wm-lh-bankssts)? I'm not completely sure but this may/may not give better results when tracking between labels as nodes. 2. Is it possible to include the subcortical structures in the final masked image? Thank you so much! Michiko On Mon, Feb 5, 2018 at 12:30 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > You mean you want to remove everything but the WM labels? You can do it in > two steps: > > 1. Create a mask of the wm labels: > > mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o > wm.mask.nii.gz > > 2. Mask the wmparc: > > mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz > > > > > On 2/4/18 5:28 PM, Michiko H. wrote: > > Hi Freesurfer experts, > > I am wondering if it is possible to remove the original labels after > extending the parcellation by 2mm into the WM for tractography? I don't > wish to have tractography run on both sets of labels considering the > algorithm would take into account the streamlines terminating at nodes > defined by the labels so it doesn't quite make sense to count streamlines > terminating at both the original label separately from the new label > extending into the WM. > > I used the following command for growing the parcellation into WM: > > mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm > --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz > > > Would appreciate help and suggestions! > > > Thanks, > > Michiko. > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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. > >
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