Hi Arsene, you did not say anything wrong. What you are trying to do is a 
research project in and of itself. To support you, we would have to put huge 
amounts of time into it, which we are not willing to do.
doug


On 9/5/2019 7:56 AM, arsene ella wrote:

        External Email - Use Caution

Dear Douglas,
I know that you are very busy by a lot of other people to support but I don't 
understand your answer about my questions and disappointed by it...
Did I say or do something wrong?
Regards,
Arsene

Le jeu. 5 sept. 2019 à 00:12, Greve, Douglas N.,Ph.D. 
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> a écrit :
Sorry, I think this is beyond our ability to support.

On 9/4/19 4:44 AM, arsene ella wrote:
>
>         External Email - Use Caution
>
> /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/
>
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