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*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 brai**ns (**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 **?**Y**ou’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 seg**mented** 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*