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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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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        contains patient information, please contact the
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Hi Gari - You're talking about thresholding the probtrackx maps, right? If so the 20% at which the tracula maps are thresholded by default is probably too high for probtrackx, I'd try something like 2%. (Tracula is global and probtrackx is local tractography, so their outputs are different beasts.)

Are the waytotal values very different among subjects? Are the anatomical seed mask sizes very different? Did you take that into account? Probtrackx will generate X sample paths for each voxel in the seed mask. Did you threshold the tracula tracts before using them as waymasks?

a.y

On Tue, 14 Jan 2014, Garikoitz Lerma-Usabiaga wrote:

Hi Anastasia, it worked perfectly and I could run probtrack between my anatomical seed and using waypoints from Tracula tracts.

I have another doubt right now. The probabilities in each new tract are very different. I divided every value with waytotal using fslmaths -div in order to normalize them, and obtained something like this:  subject: S_20, Max Value after normalizing with waytotal: 0.75533 subject: S_23, Max Value after normalizing with waytotal: 0.27883 subject: S_25, Max Value after normalizing with waytotal: 0.60251 subject: S_27, Max Value after normalizing with waytotal: 0.32355

Should I consider the same absolute value for all tracts in order to threshold them or should I threshold all tracts independently with the 20%?

I want to check visually the existence of the tract between the anatomical and the tract, with the same probability across subjects, and afterwards obtain the FA values in order to correlate with behavior.

Thanks again! Gari

On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  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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