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