External Email - Use Caution Got it :)
filling the unassigned vertices with 'unknown' using tksurfer solved my problem. cheers, Joerg > Hi Bruce, > this did not change anything. But I tried the process of mris_ca_train, > mris_ca_label with lh.oasis.chubs.annot and this worked fine. > > A closer look to my source annot file from mris_seg2annot showed that > the label 'unknown' is missing. > > How can I add the unknown to all unlabeled vertices? > > cheers, > Joerg > > > >> Hi Joerg >> >> I'm not positive that I understand, but have you tried giving >> mris_ca_label the switch: >> >> mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ... >> >> >> that should remove non-cortical regions from your output annot >> >> cheers >> Bruce >> >> On Tue, 5 Mar 2019, Jörg Stadler wrote: >> >>> External Email - Use Caution >>> Hi, >>> >>> I transfered the SPM Anatomy Toolbox >>> (http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html) >>> >>> from Collin space to fsaverage using >>> >>> Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT. >>> *Accurate nonlinear mapping between MNI volumetric and FreeSurfer >>> surface coordinate systems* >>> <http://people.csail.mit.edu/ythomas/publications/2018VolSurfMapping-HBM.pdf>, >>> >>> /Human Brain Mapping/ 39:3793–3808, 2018. >>> >>> >>> mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s >>> fsaverage --hemi rh --o rh.anat_v22c >>> >>> mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s >>> fsaverage --hemi lh --o lh.anat_v22c >>> >>> >>> This gave me the annot files for fsaverage (annotation.png) and a >>> template for the color lookup table. >>> >>> >>> Training of the classifier: >>> >>> mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot >>> fsaverage lh.Anatomy_v22c.gcs >>> >>> mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot >>> fsaverage rh.Anatomy_v22c.gcs >>> >>> >>> Transfer to individual subject fsaverage: >>> >>> mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs >>> Anatomy_v22c.annot >>> mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs >>> Anatomy_v22c.annot >>> >>> >>> Now the miracle occurred and the whole surface got labeled. >>> (mris_ca_label.png) >>> >>> How can a keep unassigned regions unlabeled? >>> >>> >>> Joerg >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Dr. rer. nat. Joerg Stadler Leibniz Institute for Neurobiology (LIN) Special Lab Non-Invasive Brain Imaging Brenneckestr. 6, D - 39118 Magdeburg Tel.: +49-391-6263-92171 Fax: +49-391-6263-92589 Gnupg-Key:http://keyserver.ubuntu.com search for E-Mail Adress Key fingerprint:B005 A785 8191 BED1 1B75 9B06 120C F20F 3E08 D20F _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
