Dear Timothy, Exactly, the goal was to have a structural connectome that has the same parcels as a functional one and covers the whole brain. The problem with the surface ROI is that I would be missing the subcortical structures, which I would like to retain. Maybe there is a simpler way of doing this that I am missing. I could compute a dense connectome and parcellate it in a second step maybe? I thought that doing a ROI to ROI approach would be simpler, but I might have been mistaken. Looking at the tutorial document, it seems I can obtain a dense connectome with the following call: probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged --mask=../T1w/Diffusion.bedpostX/nodif_brain_mask --xfm=xfms/standard2acpc_dc --invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz --loopcheck --forcedir -c 0.2 --sampvox=2 --randfib=1 --stop=Connectome/stop --wtstop=Connectome/wtstop –forcefirststep --waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 -x Connectomes/GrayOrdinates.txt --omatrix1 --dir=Connectomes I am just wondering, what are these inputs and how would I obtain them: --stop=Connectome/stop, --wtstop=Connectome/wtstop, waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 and Connectomes/GrayOrdinates.txt ?
Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Timothy Coalson <tsc...@mst.edu> Date: Friday, November 9, 2018 at 5:02 PM To: Leonardo Tozzi <lto...@stanford.edu> Cc: "Glasser, Matthew" <glass...@wustl.edu>, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk>, hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation So, it gets a little complicated, because you have to be careful about what order the different sections of seeds were put together in. I don't know how specifying multiple ROIs to probtrackx works, keeping it simple and doing a single combined surface ROI that covers all the areas you want is more likely to be usable. The likely reason for the volume loop is because in cifti, the different subcortical structures are stored as separate sections, but the entire used part of a surface is stored contiguously in vertex order. I am still missing the big picture here: why do you want to use labels to constrain the tractography? Is what you actually want an all parcels by all parcels matrix? Tim On Fri, Nov 9, 2018 at 6:37 PM, Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> wrote: Dear Timothy, Thank you very much for your quick response. To clarify some points: some ROIs were surface based and some voxel based. To create them, I followed the steps I outlined along this thread, which I am summarizing below: # creating cortical labels wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_LEFT cortL.label.gii wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_RIGHT cortR.label.gii # creating subcortical labels wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all subcort.nii.gz # creating the cortical ROIs for region in R_V1_ROI R_MST_ROI (etc.) do wb_command -gifti-label-to-roi cortR.gii $PWD/ROIs/${region}.func.gii -name $region wb_command -gifti-label-to-roi cortL.gii $PWD/ROIs/${region}.func.gii -name $region done # creating the subcortical ROIs for region in L_Amygdala R_Amygdala (etc.) do wb_command -volume-label-to-roi subcort.nii.gz $PWD/ROIs_subcort/${region}.nii.gz -name $region done # converting cortical ROIs to ASCII for region in R_V1_ROI R_MST_ROI (etc.) do surf2surf -i /Users/leonardotozzi/Desktop/DiffusionConnectivityTest/conn008/MNINonLinear/fsaverage_LR32k/conn008.R.white.32k_fs_LR.surf.gii -o $PWD/ROIs_cort/$region.asc --values=$PWD/ROIs_cort/$region.func.gii --outputtype=ASCII done Then I added all these resulting ROIs (cortical + subcortical) into the seeds.txt file, which is an input to probtrack. I am wondering if there is not something wrong with my surf2surf call. The command seems to take caret as convention by default, but are the ROIs at this point in Freesurfer space? The FDT help gives some info about additional steps to use Freesurfer ROIs here (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide) but I am unsure about whether these apply to output of the HCP pipeline. I am having difficulties navigating between all these different spaces (MNI, Freesurfer, diffusion etc.). Also, the subcortical ROIs seem to be in MNI space, which makes me wonder in what space the cortical ROIs are. About Matrix1, it’s not symmetric, I built a connectivity matrix by taking the upper triangle. I think it should track from all my ROIs to all my ROIs. Concerning wb_command -probtrackx-dot-convert, it requires a few inputs but I am not sure what files to use. I hope this adds more information, 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<mailto:lto...@stanford.edu> | (650) 5615738 From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Friday, November 9, 2018 at 4:11 PM To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Cc: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>, hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation 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<mailto: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<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Thursday, November 8, 2018 at 6:48 PM To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>, Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Thursday, November 8, 2018 at 9:17 PM To: Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:lto...@stanford.edu> | (650) 5615738 From: Stamatios Sotiropoulos <stamatios.sotiropou...@ndcn.ox.ac.uk<mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>> Date: Wednesday, October 31, 2018 at 1:38 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: Leonardo Tozzi <lto...@stanford.edu<mailto: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<mailto:glass...@wustl.edu>> wrote: Also use the label ones to make GIFTI label files. Matt. From: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, October 30, 2018 at 6:34 PM To: Matt Glasser <glass...@wustl.edu<mailto: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<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, October 30, 2018 at 4:22 PM To: Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, October 30, 2018 at 6:19 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto: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<mailto:lto...@stanford.edu> | (650) 5615738 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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<mailto: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
