Thank you Matt! Best, Nailin
2016-11-02 14:53 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>: > The fMRI data are already in standard CIFTI space. > > Peace, > > Matt. > > From: nailin yao <ynai...@gmail.com> > Date: Wednesday, November 2, 2016 at 1:52 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: Timothy Coalson <tsc...@mst.edu>, "hcp-users-request@ > humanconnectome.org" <hcp-users-requ...@humanconnectome.org>, " > hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] correlation > > 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 <glass...@wustl.edu>: > >> 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: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >> Coalson <tsc...@mst.edu> >> Date: Tuesday, November 1, 2016 at 5:06 PM >> To: nailin yao <ynai...@gmail.com> >> Cc: "hcp-users-requ...@humanconnectome.org" < >> hcp-users-requ...@humanconnectome.org>, "hcp-users@humanconnectome.org" < >> hcp-users@humanconnectome.org> >> 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 <ynai...@gmail.com> 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 >>> 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. >> > > > > -- > Nailin Yao, PhD > > Postdoctoral Associate > Department of Psychiatry, Yale University > > > ------------------------------ > > 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
