Hi Anastasia,
the problem is with mri/hippo_subfield_in_diffusion_space.nii, which originally is mri/hippo_subfield.mgz, the output of running recon-all -hippo-subfields. So as far as I understand it is not in anatomical space, according to MRI info, it is (one example):
- LIA
- 85x97x141
- 0.5x0.5x0.5

So, how could I convert it to the diffussion space in FSL format in order to be able to use it in probtrackx?
Should I do 2 steps or 3 steps?
1.- mri_convert to anatorig space (brainmask.mgz space, LIA, 256x256x256)
2.- anatorig2diff in order to change to FSL format and to diffusion space? 
(3.- would be the previous one in two steps, first from anatorig to anat and then from anat to diff)

Any indication of the best programs to do all the change will be appreciated (I've seen in trac-all.log that mostly fsl programs are being used to do the flips, and then tkregister2 and bbregister for the registrations)

Thanks for the help!
Gari 



On Sat, Jan 11, 2014 at 1:31 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

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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