Your workflow looks right. Once you have a set of labels you want to combine, use mris_label2annot. You will have to supply a color tab (--ctab) that you have modified to include the new label. To mediate between multiple labels having the same vertex, use the --maxstatwinner option. You will have to include a "stat" as the last column in the label file. This is usually 0, so change it to 1 in your custom label.
On 07/23/2018 10:13 AM, Bruce Fischl wrote: > Hi James > > yes, I guess that is the right workflow. YOu will also need to modify > the color lut to include your new parcel. As for overlap you could > just remove it in matlab I guess. Or maybe mris_label2annot handles > it, I'm not sure (Doug may know) > > cheers > Bruce > On Mon, 23 Jul 2018, James Hobart wrote: > >> >> External Email - Use Caution >> >> Good Morning All, >> Just wondering if anyone had any advice regarding this problem? I am >> still struggling to get things >> running as intended! >> >> Any help would be greatly appreciated. >> >> BW >> James >> >> >> On Tue, Jun 26, 2018 at 1:20 PM, James Hobart >> <jameshoba...@gmail.com> wrote: >> >> Hi Freesurfer community, >> >> >> >> I have an issue in adding a surface label to an annot file. >> >> I had a manually drawn .nii mask in native space for each >> subject which I have used >> mri_vol2surf to create a surface overlay and then mri_vol2label >> (with the surf argument) >> to create a surface label for the mask. >> >> >> >> I also have a custom parcellation of fsaverage which I have >> mapped to individual native >> space using mri_surf2surf. >> >> >> >> My issue is I want to combine the outputted binarymask.label >> file with the custom >> parcellation. My understanding is that I would need to combine >> the binarymask.label with >> the custom.parc.annot file. In order to do this wopuld I break >> down the annot file with >> mri_annot2label and then rebuild including the new >> binarymask.label? >> >> >> >> Could I also just add another row to the LUT from the >> custom.parc.annot file to allow >> this? >> >> >> >> And finally, how do I deal with the fact that the >> binarymask.label will overlap with >> other labels? Ideally I need to force the overwrite of vertex >> labels so that the >> binarymask.label is prioritised? >> >> >> >> BW >> >> James >> >> >> >> > > > _______________________________________________ > Freesurfer mailing list > 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 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.
