Hi Gari - The authors of probtrackx would be able to give you more information on how to normalize probtrackx outputs, but I'd suggest taking a look at the methods section of this paper as an example:

S. B. Eickhoff, S. Jbabdi, S. Caspers, A. R. Laird, P. T. Fox, K. Zilles, and T. E. J. Behrens, “Anatomical and Functional Connectivity of Cytoarchitectonic Areas within the Human Parietal Operculum,” J Neurosci, vol. 30, no. 18, pp. 6409–6421, May 2010.

Hope this helps, a.y

On Mon, 24 Feb 2014, Garikoitz Lerma-Usabiaga wrote:

Thanks Anastasia!

On Thu, Feb 6, 2014 at 1:11 AM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Hi Gari - You're talking about thresholding the probtrackx maps, right?

Yes   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.)

OK, thanks! The problem is that at 2% I think the tracts I obtain are too big. I attached a subject example (S_02) with thresholds at 2%, 5%, 20% and 30% in order to have an idea of what do you think it would be normal. The file is called tracts.png.

Inline image 2

  Are the waytotal values very different among subjects?

I think there is quite high variability, but I don't know what's normal. In the next figure, values.png, you can find the values:

• Waytotal values for the two new tracts
• Max values in the tracts after normalizing
• Seed mask size

Inline image 1

Are the anatomical seed mask sizes very different?

I don't think so. They are in values.png as well if you want to take a look.

Did you take that into account? Probtrackx will generate X sample paths for each voxel in the seed mask.

I didn't take either the waytotal or seed mask or waypoint mask sizes into account when thresholding. How would you recommend doing that?

Did you threshold the tracula tracts before using them as waymasks?

Yes, using fslmath I used -thrp 20 first to threshold them and after that I binarize it to create the waypoint.

Thank you very much for your help again, Gari

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 




                                The information in this e-mail is intended only for
                                the person to whom
                                it is
                                addressed. If you believe this e-mail was sent to
                                you in error and the
                                e-mail
                                contains patient information, please contact the
                                Partners Compliance
                                HelpLine at
                                http://www.partners.org/complianceline . If the
                                e-mail was sent to you
                                in error
                                but does not contain patient information, please
                                contact the sender
                                and properly
                                dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.