New subject: Question about how to build .gca files from non-human atlas and images

4 Sep 2019


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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*