So it isn't parcels by parcels, it is dense, but within an ROI only? If I understand the format correctly, you could use -cifti-create-dense-scalar to make a template cifti, then use that in -cifti-convert -from-text, if the text format is simple enough. If you want to expand it to the standard grayordinates, you can then do -cifti-create-dense-from-template.
Tim On Thu, Jun 23, 2016 at 6:12 PM, Glasser, Matthew <[email protected]> wrote: > Hi Longchuan, > > I think you will need to use matlab for this. You can make a dscalar that > contains the PFC_L ROI as ones. Then you can map the vertices in that ROI > to the rows? in the asc file and put the values in the appropriate > locations. Then save the file back out and view it in Connectome > Workbench. We will think about whether we cn make this easier in > wb_command. > > Peace, > > Matt. > > From: Longchuan Li <[email protected]> > Reply-To: Longchuan Li <[email protected]> > Date: Thursday, June 23, 2016 at 4:54 PM > To: Matt Glasser <[email protected]>, HCP Users < > [email protected]> > Subject: Re: [HCP-Users] Visualize outputs of seeds to targets > classification in workbench > > Hi, all > > Sorry for sending several identical emails, as I repeatedly got replies > saying my emails are waiting to be approved. > > So, basically I have four ROIs: PFC_L.border, ATC_L.border; IPL_L.border > and OC_L.border. I want to parcellate PFC_L, according to the connectivity > inputs from the other three ROIs. So, I run 'probtrackx2', with PFC_L as > the seed and other three as the targets. As all files are surface files, > after the run, I get several files like below: > seeds_to_ATC.gii.asc > seeds_to_IPL.gii.asc > ... > > However, I find that workbench cannot read these standard ASCII files. So > my question is how I can read these surface files from FSL in workbench? > > I kind of figured out a workaround after I posted the question: it seems > that a file called "matrix_seeds_to_all_targets" contains N*P matrix, with > N being the number of vertex in the seed mask and P being the number of > target masks. The values seem to be the number of connected streamlines. > So, I may write a simple matlab script to parcellate the seed mask myself > by using "winner-take-all" strategy, based on the matrix and their > corersponding vertex on the surface. > > If you know any better ways, please let me know. > > Many thanks > Longchuan > > > On Thursday, June 23, 2016 5:32 PM, "Glasser, Matthew" <[email protected]> > wrote: > > > Hi Longchuan, > > Can you give some details on what the seeds and targets are? > > Peace, > > Matt. > > From: <[email protected]> on behalf of Longchuan Li < > [email protected]> > Reply-To: Longchuan Li <[email protected]> > Date: Thursday, June 23, 2016 at 9:31 AM > To: HCP Users <[email protected]>, " > [email protected]" <[email protected]> > Subject: [HCP-Users] Visualize outputs of seeds to targets classification > in workbench > > > > Hi, HCP experts > > I searched this topic in the mailing list for a while and seem not have > found the answer: after I performed seed-to-target analyses in probtrackx2 > using surface-based ROIs, how can I convert the results > "seed_to_target_ROIs.asc" to a format that is supported by Workbench and > could be loaded and visualized in WB? > > Thank you in advance! > Longchuan > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > 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 > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
