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]<mailto:[email protected]>> Reply-To: Longchuan Li <[email protected]<mailto:[email protected]>> Date: Thursday, June 23, 2016 at 4:54 PM To: Matt Glasser <[email protected]<mailto:[email protected]>>, HCP Users <[email protected]<mailto:[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]<mailto:[email protected]>> wrote: Hi Longchuan, Can you give some details on what the seeds and targets are? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Longchuan Li <[email protected]<mailto:[email protected]>> Reply-To: Longchuan Li <[email protected]<mailto:[email protected]>> Date: Thursday, June 23, 2016 at 9:31 AM To: HCP Users <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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]<mailto:[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
