Hi Gari - So if I understand correctly, your inputs to probtrackx are:
mri/hippo_subfield_in_diffusion_space.nii
dmri.bedpostX/merged
dmri.bedpostX/nodif_brain_mask
If these all come from the output of tracula, aren't these all in LAS
orientation?
a.y
On Thu, 9 Jan 2014, 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
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
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