What is the error with ciftiopen? Also have you run wb_command -cifti-parcellate successfully?
Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Ferdaus Kawsar <ferdaus.kaw...@gmail.com<mailto:ferdaus.kaw...@gmail.com>> Date: Thursday, August 11, 2016 at 3:35 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] Extract average time-course from cortical parcels Hi Tim, Thanks for your reply. I used cifti-separate as you suggested to create volumes from *.dtseries.nii file I have. However, I am having difficulty to read the resultant file. Is it a cifti file? I cannot read this file using either ft_read_cifti() or ciftiopen(). Also the file is huge (1.8 GB). How do I extract time-course from this file? I created the file using following command: wb_command -cifti-separate '*.dtseries.nii' COLUMN -volume PUTAMEN_RIGHT 'out_putament_right' Best -Ferdaus On Wed, Aug 10, 2016 at 5:42 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: You might want to use "wb_command -cifti-parcellate" to do this for you, it has some extra options to do things like weighted means according to vertex area. Manually matching things up in matlab from loaded cifti files may be difficult, as some .dlabel.nii files don't exclude the medial wall, and may not include the subcortical voxels that the .dtseries.nii files do. You can use -cifti-separate on cifti files to make simpler single-hemisphere full-surface gifti files, and a nifti volume file for the subcortical stuff (though doing this on the timeseries will result in a fairly large volume file when loaded in memory). Tim On Wed, Aug 10, 2016 at 2:48 PM, Ferdaus Kawsar <ferdaus.kaw...@gmail.com<mailto:ferdaus.kaw...@gmail.com>> wrote: Hi HCP Team, I was wondering if someone could help regarding a task I am trying to do. I need to extract average time-course for both cortical and sub-cortical parcels. I was able to extract average time-courses for sub-cortical parcels. After I loaded my *dtseries.nii cifti files (using ft_read_cifti()) in matlab, I could access all the time-courses for sub-cortical regions. There are 19 sub-cortical regions. After I got all the time -courses for a sub-cortical region, a simple mean() method in matlab gave me the average time-course. I am curious if this approach is right? Also, how do I get the time-courses for a cortical parcel? My eventual goal is to extract average time course for each of 180 parcels in each hemisphere. Best regards, -Ferdaus -- Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
