Is there anyway I can do the surface-to-surface tractography myself given the data provided in https://balsa.wustl.edu/study/show/W336. I can see there is a fiberTEMP.nii file there but I do not know if I can run probtrackx using it.
Regards, Kamal From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Wednesday, February 28, 2018 at 6:56 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wbsparse Also beware, since one of the dimensions is white matter voxels, the dconn from -convert-matrix4-to-matrix2 will be larger than a standard 91k dconn (78GB based on the information you posted, versus ~30GB for a 91k dconn). Surface-to-surface tractography would normally be done with a different output format. You may be able to approximate it with a hack by generating a volume ROI just inside the white matter surface, but that will be somewhat angle-dependent in its response, so I wouldn't trust it much. Tim On Wed, Feb 28, 2018 at 5:04 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: wb_command -convert-matrix4-to-matrix2 will convert wbsparse to a dense connectome file. I’m not sure you can actually do what you are asking, because all that is stored are counts of streamlines that use a particular fiber orientation in a voxel. Peace, Matt. From: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Wednesday, February 28, 2018 at 5:00 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wbsparse Yes, It’s in https://balsa.wustl.edu/study/show/W336. From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Wednesday, February 28, 2018 at 5:28 PM To: "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] wbsparse Did you get that from BALSA? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Shadi, Kamal" <kamal.shad...@gatech.edu<mailto:kamal.shad...@gatech.edu>> Date: Wednesday, February 28, 2018 at 4:25 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] wbsparse Hi All, Is there anyway I can use trajTemp.wbsparse file to extract connectivity information between a vertex on a surface and an ROI in gift label file (streamline count in particular)? The information of trajTemp file is as follows: Name: pm1.trajTEMP.wbsparse Type: Connectivity - Fiber Trajectory TEMPORARY Structure: CortexLeft CortexRight Cerebellum AccumbensLeft AccumbensRight AllGreyMatter AllWhiteMatter AmygdalaLeft AmygdalaRight BrainStem CaudateLeft CaudateRight CerebellarWhiteMatterLeft CerebellarWhiteMatterRight CerebellumLeft CerebellumRight CerebralWhiteMatterLeft CerebralWhiteMatterRight Cortex DiencephalonVentralLeft DiencephalonVentralRight HippocampusLeft HippocampusRight Invalid Other OtherGreyMatter OtherWhiteMatter PallidumLeft PallidumRight PutamenLeft PutamenRight ThalamusLeft ThalamusRight Maps to Surface: false Maps to Volume: true Maps with LabelTable: false Maps with Palette: false CIFTI Dim[0]: 650534 CIFTI Dim[1]: 32492 ALONG_ROW map type: BRAIN_MODELS Has Volume Data: true Volume Dims: 225,293,186 Volume Space: -0.43,0,0,48;0,0.43,0,-64;0,0,0.43,-48 AccumbensLeft: 591 voxels AccumbensRight: 575 voxels AmygdalaLeft: 1894 voxels AmygdalaRight: 1669 voxels BrainStem: 22490 voxels CaudateLeft: 3433 voxels CaudateRight: 3293 voxels CerebellarWhiteMatterLeft: 4665 voxels CerebellarWhiteMatterRight: 4685 voxels CerebellumLeft: 22753 voxels CerebellumRight: 27627 voxels CerebralWhiteMatterLeft: 92543 voxels CerebralWhiteMatterRight: 93079 voxels CortexLeft: 159552 voxels CortexRight: 161301 voxels DiencephalonVentralLeft: 4361 voxels DiencephalonVentralRight: 3784 voxels HippocampusLeft: 4503 voxels HippocampusRight: 4413 voxels PallidumLeft: 2183 voxels PallidumRight: 2320 voxels PutamenLeft: 8039 voxels PutamenRight: 7422 voxels ThalamusLeft: 6502 voxels ThalamusRight: 6857 voxels ALONG_COLUMN map type: BRAIN_MODELS Has Volume Data: false CortexLeft: 32492 out of 32492 vertices _______________________________________________ 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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
