On 01/09/2014 12:45 PM, Garikoitz Lerma-Usabiaga wrote:
> 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

That looks right, though I would use mri_label2vol as it will be more
accurate than mri_vol2vol for segmentations.

>
> 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).

Yes I think so.

I'll leave the last question to AY

>
>
> 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
>
>

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