Dear Freesurfer experts,

I’ve built an atlas of structures of a non-human average brain and now I would like to build its .gca files from scratch. From the Freesurfer mailing list, I saw that this is possible using rebuild_gca_atlas.csh which trains labelled brains (seg_edited.mgz) and their intensity volumes (it is said to use the norm.mgz for this purpose) from several subjects through mri_ca_train. My questions are :
1) How to normalize my native intensity volume to a norm.mgz  volume without .gca and .lta files asking by  mri_ca_normalize ?
You’ve suggested to give  mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca by trying -seg <manual seg volume>. Then the gca name won't matter - it should ignore it… I tried this as followed :
let : 
- Brain_Template_T1_MPR.mgz               be my intensity native volume
- Brain_Cortex_Atlas.mgz                        be my manual segmented volume
- Brain_Template_T1_MPR_norm.mgz    be my norm output volume

Command lines :
mri_ca_normalize      Brain_Template_T1_MPR.mgz    -seg Brain_Cortex_Atlas.mgz     Brain_Template_T1_MPR_norm.mgz
gave the following error message :
reading 1 input volume
reading atlas from '-seg'...
GCAread(-seg): could not open file
No such file or directory
mri_ca_normalize: could not open GCA -seg.
No such file or directory

mri_ca_normalize     -seg   Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR.mgz     Brain_Template_T1_MPR_norm.mgz
gave the following message  and stopped:
using segmentation volume /home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to generate control points...
usage: mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...

What is wrong with theses mri_ca_normalize commands ?

2) My second question is to know how to transfert labels from my manual segmented volume (ex : atlas.mgz) to each single image volume (ex : vol1.mgz) ?
You’ve suggested to use mri_label2label, but I didn’t see anything allowing me to do a volume_to_volume transfert from its –help… If I got it wrong, could you suggest a command ?

cheers

Arsene