Make sure that the names in the ctab match the names of the label files. If you run it on a few labels with --l instead, does it generate an annot?

On 6/12/17 7:37 PM, Almarshad F. wrote:

Hi FreeSurfer team;

i'm having diffuculty in creating the annotation file.. i had put all the labels i need to use the file and equal_parcellation_lh, and prepared my LUtable.txt .. when i run the command mris_label2annot it creates an empty annot file with 0 labels .. below is the command and its result ..

mris_label2annot --s NMI --h lh --no-unknown --ctab NMI/label/equal_parcellation_lh/mylut.txt --a laparc --ldir NMI/label/equal_parcellation_lh Reading ctab NMI/label/equal_parcellation_lh/mylut.txt Number of ctab entries 41 INFO: no labels specified, generating from ctab

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs cmdline mris_label2annot --s NMI --h lh --no-unknown --ctab NMI/label/equal_parcellation_lh/mylut.txt --a laparc --ldir NMI/label/equal_parcellation_lh sysname Linux hostname fatima-DQ67SW machine x86_64 user fatima

subject NMI hemi lh SUBJECTS_DIR /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs ColorTable NMI/label/equal_parcellation_lh/mylut.txt AnnotName laparc nlables 0 LabelThresh 0 0.000000 Loading /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs/NMI/surf/lh.orig Writing annot to /home/fatima/Downloads/tutorial_data/buckner_data/tutorial_subjs/NMI/label/lh.laparc.annot

any help will be much appreciated

regards; Fatima

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer