Re: [HCP-Users] Some questions about the usage of Connectome Workbench

[Harms, Michael]

I just checked, that S900 group average package includes the following: S900.All.midthickness_MSMAll_va.32k_fs_LR.dscalar.nii S900.midthickness_MSMAll_va.32k_fs_LR.dscalar.nii S900.midthickness_MSMAll_va_ratio.32k_fs_LR.dscalar.nii The first contains the midthickness vertex areas for all subjects.  The 2nd is the average across those subjects. Matt: What does the *va_ratio* file represent? --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Glasser, Matthew" <glass...@wustl.edu> Date: Sunday, May 22, 2016 at 7:57 PM To: Aaron C <aaroncr...@outlook.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Some questions about the usage of Connectome Workbench These days we use the group average surfaces and correct for group averaging shrinkage with the appropriate vertex areas.  Hopefully those files were included in the release: ${StudyFolder}/${Group}/MNINonLinear/fsaverage_LR32k/${Group}.midthickness${RegName}_va.32k_fs_LR.dscalar.nii, which you can split out into GIFTI shape files with wb_command -cifti-separate for use in commands that want a GIFTI file. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Aaron C <aaroncr...@outlook.com> Date: Sunday, May 22, 2016 at 7:52 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Some questions about the usage of Connectome Workbench Thank Tim and Jennifer very much for your answers! I have one more question about the spatial operation commands of Connectome Workbench. If I use the commands “-cifti-gradient” or “-cifti-smoothing” for processing HCP group-averaged maps, should I use the atlas midthickness surfaces (“Conte69.L.midthickness.32k_fs_LR.surf.gii” and “Conte69.R.midthickness.32k_fs_LR.surf.gii”) or HCP S900 group-averaged surfaces (“S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii” and “S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii”) for the input arguments of these commands? Thank you! From: e...@wustl.edu To: aaroncr...@outlook.com; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Some questions about the usage of Connectome Workbench Date: Fri, 20 May 2016 21:22:16 +0000 HI Aaron, In answer to your #2 question... There are S900 group average data and surfaces available in the 900 Subjects Group Average Data section of the HCP S900 project page in ConnectomeDB https://db.humanconnectome.org/data/projects/HCP_900 Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu www.humanconnectome.org From:hcp-users-boun...@humanconnectome.org <hcp-users-boun...@humanconnectome.org> on behalf of Aaron C <aaroncr...@outlook.com> Sent: Friday, May 20, 2016 3:23:48 PM To: hcp-users@humanconnectome.org Subject: [HCP-Users] Some questions about the usage of Connectome Workbench   Dear HCP experts, I have some questions about the usage of Connectome Workbench for displaying custom group-level ICA maps stored in a *.dtseries.nii file. 1.    I am currently able to save the figure (similar to the format of the figure displayed in Scene 3 of Connectome Workbench v1.0 Tutorial) of each component map of a group ICA *.dtseries.nii file by clicking on “File>Capture Image” manually and then change to the next component map and do the same again manually, but this way is petty time-consuming if I have a lot of ICA components (frames) in a *.dtseries.nii file. How could I batch export these surface view figures via Connectome Workbench by using some commands?   2.    I found R440 group-averaged surface files in the WB 1.0 Tutorial Dataset. However, are there any S900 group-averaged surface files available for use in the HCP dataset? 3.    How could I get the anatomical region name (in terms of Brodmann or any other brain atlases) of each grayordinate above a user-defined threshold in a custom map using Connectome Workbench (similar to the function of clicking “Report” button of xjView)? Thank you very much! _______________________________________________ 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   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 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. 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users