Sorry, I think this is beyond our ability to support.
On 9/4/19 4:44 AM, arsene ella wrote:
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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/
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