Hi Gabriel what are you trying to achieve? There's no point in building a gca from a single average subject. The gca is typically built be compiling statistics across many subjects.
Not sure if you need the answers any longers but (1) you can view the gca with freeview as it if were an image file (append #0 and #1 for viewing different "frames", in this case that denotes max probability label and mean intensity of that label). (2) the norm.mgz definitely shouldn't be empty, and (3) yes, mri_ca_label would be the right tool cheers Bruce On Wed, 2 Jan 2013, Gabriel Gonzalez Escamilla wrote: > Dear FreeSurfer experts > > Happ new year to all of you, and thanx for all your help along the past 2012. > > I would like to make some questions regardins a new atlas creation > > 1) In a first step before mri_ca_train I did use mri_ca_normalize to > normalize my FS_MNI152average subject > to the JHU.ICBMtracts.1mm.mgz but this create an empty norm.mgz, is this > normal? > whean I saw that the norm.mgz was empty I decide to create all the files by: > recon-all -s My_MNI152_avg -autorecon1 -autorecon2-inflate1, that create all > files as normally does with > my every other subjects; > > Then I run mri_ca_train, using as -mask the brain.mgz, as -T1 the norm.mgz > created during recon-all, > directed to my FS_MNI251average subject, and as -parc_dir > JHU.ICBMtracts.1mm..mgz; as result got the .gca > and a mgh file > I use the load_gca.m to check the .gca created, but get the next error > message: > "version 5 in file $JHU.ICBMtracts_12_2012.gca incorrect - not a known gca > file" > 2) Is there any way to check at the gca file created? just to make myself > sure that everything is placed > in the right way > > 3) And lastly, Which is the next step to parcellate the WM of all my subjects > as the new atlas? Can I use > this gca file with mris_ca_label? or some other tool will be better? > > > Many thanks in advanced, > Gabriel. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
