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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> 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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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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