Thank you Tim and Matt, So when I extract hippocampus from Atlas_ROIs.2.nii.gz, and use it as roi to do -cifti-average-roi-correlation on one of the subject, does the ROI automatically overlay on the native subcortical space of that subject, or normalized space which is the same for everyone? Thank you!
Best, Nailin 2016-11-01 19:15 GMT-04:00 Glasser, Matthew <[email protected]>: > I think he wants to do a correlation of an ROI of the hippocampus. There > you would benefit from doing as Tim suggests, but then using > wb_command -cifti-average-roi-correlation > > Peace, > > Matt. > > From: <[email protected]> on behalf of Timothy > Coalson <[email protected]> > Date: Tuesday, November 1, 2016 at 5:06 PM > To: nailin yao <[email protected]> > Cc: "[email protected]" <hcp-users-request@ > humanconnectome.org>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] correlation > > One way to do this is to use -cifti-separate on a small 91k grayordinates > cifti with "-volume HIPPOCAMPUS_LEFT <data-dont-care> -roi <roi-output>" > and similar for right hippocampus, then combine the left and right ROIs > with -volume-math. You could also extract the labels from the > Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz file > with -volume-label-to-roi. > > Tim > > > On Tue, Nov 1, 2016 at 4:49 PM, nailin yao <[email protected]> wrote: > >> Hi, >> >> I'm trying to do an overall correlation from hippocampus on cifti file ( >> >> rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii), and I run the command: >> >> >> ./wb_command -cifti-correlation /Users/ny87/temp/S0009QPW/MNIN >> onLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii >> /Users/ny87/temp/S0009QPW/MNINonLinear/try_hipp_corr.dscalar.nii >> -roi-override -vol-roi /Users/ny87/temp/S0009QPW/MNIN >> onLinear/try_output_hipp.nii >> >> >> which result is ERROR: roi volume space doesn't match cifti volume space. >> >> >> May I know which atlas file is the right one to extract hippocampus ROI ? >> >> >> Thank you very much! >> >> >> Best, >> >> Nailin >> >> -- >> Nailin Yao, PhD >> >> Postdoctoral Associate >> Department of Psychiatry, Yale University >> >> _______________________________________________ >> 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 > > > ------------------------------ > > 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. > -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
