Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20.

a.y

On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote:

Thanks Anastasia, I finally got it, I had to do mri_vol2vol twice to have it
in the diffusion space. 
I have an additional question: 
I want to create waypoint masks for probtracx from Tracula tracts (for
example, uncinate). 

Should I use mri_binarize on path.pd.nii to create the mask?
Should I use 20% of the maximum value as the threshold in order to do so? (a
little help with the command line will be greatly appreciated)

thanks again!
Gari


On Sun, Jan 12, 2014 at 3:08 AM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

      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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