Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-06 Thread Bruce Fischl
are they currently labeled 0? Where did you get your color LUT from? On Wed, 6 Mar 2019, Jörg Stadler wrote: External Email - Use Caution 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 c

Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-06 Thread Jörg Stadler
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 work

Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-05 Thread Jörg Stadler
External Email - Use Caution 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 c

Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

2019-03-05 Thread Bruce Fischl
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: