There is wb_command -probtrackx-dot-convert which should be able to convert the fdt_matrix1.dot file, which should allow a better visualization of the results. I'm not entirely clear on the arguments to your probtrackx command, or what the actual ROIs you used are, but it looks like they were purely voxel-based. You may need to take something the nodif_brain_mask and turn it into a label volume with the label name set to "OTHER" (just as a placeholder that should work), and then we can figure out whether each voxel list needs to be on a row or a column option (you may need to do something manually to get one of the voxel lists, depending on the details of what matrix1 does).
I don't know the specifics of matrix1, Stam or Matt can you give me the details (is it symmetric, and if so is it stored as lower-triangle, what it actually tracks from and to)? Tim On Fri, Nov 9, 2018 at 4:58 PM, Leonardo Tozzi <lto...@stanford.edu> wrote: > Dear Matthew, > > > > Thank you, I am rerunning the tractography with that flag (it will take a > while). > > In the meantime, I have taken the coordinate file from the output > (“coords_for_fdt_matrix1”, which I think for each seed reports its > coordinates and in which ROI it is), averaged all coordinates with the same > label and used Matlab graph plotting functions to see if the centers of the > seeds resembled a cortical surface. > > I am attaching a few images of this. Image 1 shows the nodes from a view > that does resemble a coronal section, with no nodes between the > hemispheres. Image2 shows the nodes from another perspective. Image3 shows > a graph with the nodes + edges from the connectivity matrix (thresholded at > >1000 fibers). > > All in all, I think I do get something that looks like a brain, but I am > concerned with a cluster of points that seem outliers with respect to their > coordinates. You can see them in all three images and they are especially > apparent in the 3rd, since they seem to be connected to many of the > cortical regions. My fear is that these could be the subcortical regions, > that for some reason have completely different coordinates. > > Does this make sense to you? Is there some transformation I should apply > to the subcortical volumes? The subcortical ROIs I enter in the analysis > are in MNI space and not in ascii format (they are .nii.gz). Maybe there is > something I am missing, and this could simply be an issue of visualization > of the output coordinates? > > I would welcome your help. > > Thank you very much, > > > > > > > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > > > *From: *"Glasser, Matthew" <glass...@wustl.edu> > *Date: *Thursday, November 8, 2018 at 6:48 PM > *To: *Leonardo Tozzi <lto...@stanford.edu>, Stamatios Sotiropoulos < > stamatios.sotiropou...@ndcn.ox.ac.uk>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > > *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical > and subcortical parcellation > > > > I would include --opd so you can see the sum of all tracts in the volume > and make sure that looks reasonable. > > > > Matt. > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Leonardo > Tozzi <lto...@stanford.edu> > *Date: *Thursday, November 8, 2018 at 9:17 PM > *To: *Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical > and subcortical parcellation > > > > Dear all, > > > > Following the very useful guide, I have managed to run the complete ROI to > ROI tractography. > > However, I am not sure how to visualize my tracts from the output of > probtrackx2. In particular, I would like to make sure that my seeds have > been imported in the correct space as well as my CSF mask for the avoid > flag. > > As in the manual, after running bedpostx, my call of probtrackx2 was as > follows: > > > > probtrackx2 > --samples=DiffusionConnectivityTest/conn008/Diffusion/data.bedpostX/merged > --mask=DiffusionConnectivityTest/conn008/Diffusion/data.bedpostX/nodif_brain_mask > --seed=DiffusionConnectivityTest/ROIcreation/allseeds.txt --xfm= > DiffusionConnectivityTest/conn008/MNINonLinear/xfms/standard2acpc_dc > --invxfm=DiffusionConnectivityTest/conn008/MNINonLinear/xfms/acpc_dc2standard > --seedref=DiffusionConnectivityTest/conn008/MNINonLinear/T1w_restore.2.nii.gz > --loopcheck --forcedir --network --omatrix1 --avoid= > DiffusionConnectivityTest/ROIcreation/T1w_restore_brain_seg_0.nii.gz -V 1 > --dir=Network > > > > allseeds.txt is the list of the ASCII converted surfaces and volumes. In > particular, I would like to be sure that I picked the right inputs for –xfm > and –invxfm. The outputs of bedpost and the masks I created are not in the > same space. As per manual, the segmented CSF is in standard MNI space. Am I > correct in assuming that the output of bedpost (after the minimal diffusion > preprocessing) is aligned with respect to the ACPC and what the command is > doing “under the hood” is taking the transformation from MNI to this space > and applying it to the masks I specified? Also, how are the ROIs affected > by all this, considering I created them with the surf2surf command giving > as input the conn008.R.white.32k_fs_LR.surf.gii and the gifti files from > the atlas? I am a bit confused about how all these images in different > space come together. > > Also, would anyone know of a way to visualize my masks and/or the tracts > to make sure the tractography ran as intended? After running probtrackx2 I > get the following outputs: > > > > coords_for_fdt_matrix1 > > fdt_matrix1.dot > > fdt_network_matrix > > probtrackx.log > > tmpnetmaskfile > > waytotal > > > > fdt_network_matrix is my connectivity matrix of interest, with what I > assume is the number of streamlines. I think the file I would need is > “coords_for_fdt_matrix1” would anyone have any tips on how to visualize > these coordinates on the diffusion data or any other suggestion to check > the positioning of the seeds and the tractography results? > > Thank you very much, > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > > > *From: *Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk> > *Date: *Wednesday, October 31, 2018 at 1:38 AM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Cc: *Leonardo Tozzi <lto...@stanford.edu> > *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical > and subcortical parcellation > > > > Hi > > > > The HCP course tractography practical would be a good way to start (see > page 386 onwards): > > > > https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7 > > > > Briefly, if you have a number of surfaces (need to convert them to ASCII > using surf2surf) and subcortical volumes you can merge them into text files > and use those as seeds. This will get you a dense connectome which you can > then parcellate using any parcellation scheme you would like. > > > > Best wishes > > Stam > > > > > > > On 30 Oct 2018, at 23:35, Glasser, Matthew <glass...@wustl.edu> wrote: > > > > Also use the label ones to make GIFTI label files. > > > > Matt. > > > > *From: *Leonardo Tozzi <lto...@stanford.edu> > *Date: *Tuesday, October 30, 2018 at 6:34 PM > *To: *Matt Glasser <glass...@wustl.edu> > *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical > and subcortical parcellation > > > > Dear Matthew, > > > > Thank you for the very quick response. > > So for clarification, you would use the following command: > > > > wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all > subcort.nii.gz > > > > To obtain the subcortical volumes. > > What about the cortical ones? Is the file > Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii > already usable as input to FSL? I thought I would need a .gii file. Or do I > need to use the option in wb_command -cifti-separate: > > > > [-label] - repeatable - separate a surface model into a surface label file. > > In this case, what would be the argument for “<structure> - the structure to > output” ? > > Thank you very much, > > > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > > > *From: *"Glasser, Matthew" <glass...@wustl.edu> > *Date: *Tuesday, October 30, 2018 at 4:22 PM > *To: *Leonardo Tozzi <lto...@stanford.edu>, "hcp-users@humanconnectome.org" > <hcp-users@humanconnectome.org> > *Subject: *Re: [HCP-Users] Diffusion connectivity matrix with cortical > and subcortical parcellation > > > > I would separate the CIFTI file into GIFTI and NIFTI components with > wb_command -cifti-separate and follow the instructions for surface tracking > on FSL’s website. > > > > Matt. > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Leonardo > Tozzi <lto...@stanford.edu> > *Date: *Tuesday, October 30, 2018 at 6:19 PM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *Subject: *[HCP-Users] Diffusion connectivity matrix with cortical and > subcortical parcellation > > > > To Whom it may concern, > > > > I have created a dlabel file by adding to the Glasser Parcellation from BALSA > the subcortical regions of the Freesurfer atlas. > > Now my goal would be to run a tractography analysis and obtain structural > connectivity matrices using this cortical+subcortical parcellation. Could > you suggest the simplest way to go from my dlabel file to something that is > compatible with diffusion software? I know that probtrackx accepts GIFTIs > as input, but I was wondering about how to extend this to subcortical > areas. Or rather would the simplest solution be to convert each subject’s > parcellation into a series of NIFTI files in native/standard space and > input these as ROIs into probtrackx? In this case, could you recommend the > correct series of workbench commands? I am also open to other software > recommendations besides the FSL suite. > > Thank you very much, > > > > > > > > Leonardo Tozzi, MD, PhD > > Williams PanLab | Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > <https://maps.google.com/?q=401+Quarry+Rd&entry=gmail&source=g> > > lto...@stanford.edu | (650) 5615738 > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
