Hi Alex,

try a space between lh and sphere.reg

Bruce

On Wed, 21 Dec 2005, Fornito, Alexander wrote:

That worked - thank you so much!! I tried to run mris_ca_train on 4 subjects as an intial test and it seems to want a ?h.sphere.reg.smoothwm file, that I've never come across before. The output is below. Thanks again for your help.

mris_ca_train -n 2 -t /usr/local/freesurfer-dev20050905/alex_ACC_colour_LUT.txt lh.sphere.reg lh_acc.annot 1000040 1000054 1000001 1000050 lh_acc_template.gcs computing means for 3 subject processing subject 1000054, 1 of 3... MRISread(/data/flanders/work/alex/freesurfer/subjects_fe/1000054/surf/lh.sphere.reg.smoothwm): could not open file No such file or directory mris_ca_train: could not read surface file /data/flanders/work/alex/freesurfer/subjects_fe/1000054/surf/lh.sphere.reg.smoothwm for 1000054 No such file or directory

Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 21/12/2005 1:38 AM To: Fornito, Alexander; freesurfer@surfer.nmr.mgh.harvard.edu Subject: re: annotations

Hi Alex,

sorry, this was our fault - we gave you an incomplete description of how to create a .annot file. When you export an annotation, it exports all labels *that have been assigned to a structure* into the .annot file. The way you do the assignment is you bring up the labels window (window->view->labels), and assign each label to a structure and it's associated color. If you want to modify the set of available structures (and their colors), then you should create a new file in the same format as $FREESURFER_HOME/FreeSurferColorLUT.txt

and do file->load color table in tksurfer I think.

Kevin: anything to add to this?

sorry for the confusion.

Bruce