Hi Anastasia, I want to use a hippocampal subfield as a seed in FSL. I am having problems understanding how to change spaces around...
1.- Is this command ok? mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ mri/hippo_subfield_in_anatomical_space.mgz --inv --interp nearest --o mri/hippo_subfield_in_diffusion_space.nii --reg dmri/xfms/anatorig2diff.bbr.dat --no-save-reg
2.- I would like to visualize it in freeview in anatomical space to check if it is ok, if I load nu.mgz and hippo_subfield_in_anatomical_space.mgz and then load hippo_subfield_in_diffusion_space.nii with the registration file dmri/xfms/anatorig2diff.bbr.dat, should I visualize it ok? If I don't register it, they show to be displaced (more than expected).
3.- Afterwards I want to run probtracx with the following command (my doubt is mainly about the files to use, since FSL files are RAS, freesurfer anatomical are LIA and freesurfer diffusion are LIA, are all the files in the same format and FSL is ok with it?): /usr/local/fsl/bin/probtrackx --mode=seedmask -x mri/hippo_subfield_in_diffusion_space.nii -s dmri.bedpostX/merged -m dmri.bedpostX/nodif_brain_mask -o fdt_paths_hippo_subfields --dir=FSL_ConnResults_Hipp -c 0.2 -S 2000 --steplength=0.5 -P 5000 --opd
many thanks! Gari