The fiberTemp.nii file doesn't contain the specific data that probtrackx needs, so no. It contains orientation distribution parameters suitable for visualization, while probtrackx expects many precomputed direction samples - the visualization distribution is an approximation based on those.
Tim On Wed, Feb 28, 2018 at 6:25 PM, Shadi, Kamal <kamal.shad...@gatech.edu> wrote: > 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> > Date: Wednesday, February 28, 2018 at 6:56 PM > To: "Glasser, Matthew" <glass...@wustl.edu> > Cc: "Shadi, Kamal" <kamal.shad...@gatech.edu>, " > hcp-users@humanconnectome.org" <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> > 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> >> Date: Wednesday, February 28, 2018 at 5:00 PM >> To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" < >> 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> >> Date: Wednesday, February 28, 2018 at 5:28 PM >> To: "Shadi, Kamal" <kamal.shad...@gatech.edu>, " >> hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: Re: [HCP-Users] wbsparse >> >> Did you get that from BALSA? >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Shadi, >> Kamal" <kamal.shad...@gatech.edu> >> Date: Wednesday, February 28, 2018 at 4:25 PM >> To: "hcp-users@humanconnectome.org" <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 >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> _______________________________________________ >> 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
