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 lto...@stanford.edu<mailto: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<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 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 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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