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.
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