Hi,
I have several labels drawn on the white surface of average7 (ancient project). I want to generate one annotation file per hemisphere comprising these labels only in order to use mri_aparc2aseg --labelwm and then compute the volume of the underlying WM of each label. Please see the employed strategy below.
The annotation file overlaid the subject's surface is indeed reasonable, both in terms of locations and labels. After running mri_aparc2aseg, though, the resulting segmentation does not label the areas correctly. That is, the localizations of all areas are ok, but the labels (namings) are wrong. Left hemi is ok, but all five labels in the right hemi are called rh_unknown. Thus also the output from the subsequent mri_segstats is incorrect for right hemi. What am I doing wrong?
Thank you very much!
What I have done is the following:
#A. map average7 label to individual subject surface per hemi mri_label2label --srclabel average7/label/${leftlabel} \ --srcsubject average7 \ --trgsubject ${s} \ --trglabel ${s}/label/${leftlabel} \ --regmethod surface --hemi lh
mri_label2label --srclabel average7/label/${rightlabel} \ --srcsubject average7 \ --trgsubject ${s} \ --trglabel ${s}/label/${rightlabel} \ --regmethod surface --hemi rh
#B. generate annotation from several labels for each hemi (FreeSurferColor files attached) mris_label2annot --s ${s} \ --h lh --ctab FreeSurferColorLUT_Left.txt \ --l ${s}/label/APOE_ERP_grupper_left_lat_front_pole.label \ --l ${s}/label/APOE_ERP_grupper_left_OccTemp.label --a APOE
mris_label2annot --s ${s} \ --h rh --ctab FreeSurferColorLUT_Right.txt \ --l ${s}/label/APOE_ERP_grupper_right_lat_front_pole.label \ --l ${s}/label/APOE_ERP_grupper_right_OccTemp.label \ --l ${s}/label/APOE_ERP_grupper_right_med_front_pole.label \ --l ${s}/label/APOE_ERP_grupper_right_TPJ.label \ --a APOE
#C. segmenting WM based on the generated annot files mri_aparc2aseg --s ${s} --ribbon --o APOE.mgz --annot APOE --labelwm --rip-unknown
Cheers, Lars
FREESURFER_HOME: /psyklab/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5
RedHat release: Red Hat Enterprise Linux Client release 5.2 (Tikanga)
Kernel info: Linux 2.6.18-92.el5 x86_64