Has mri/hippo_subfield_in_diffusion_space.nii been actually transformed to diffusion space by applying the anatorig2diff transformation? I'm assuming that your diffusion data is not 0.5mm resolution? You can search for the name of the transformation in trac-all.log to see examples of how it is applied to volumes.

On Sat, 11 Jan 2014, Garikoitz Lerma-Usabiaga wrote:

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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