Thank you for your prompt response. Yes, this is whole brain data with full coverage of the CIFTI grayordinates space. I have not tried just running the HCP minimal preprocessing pipelines and ICA+FIX cleanup.
From: "Glasser, Matthew" <glass...@wustl.edu> Date: Wednesday, May 17, 2017 at 5:50 PM To: Leah Moreno <mmorenoort...@icloud.com>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] NaNs and grayordinates with constant timeseries Do you have those issues if you just run the HCP minimal preprocessing pipelines and ICA+FIX cleanup? I am guessing the issue lies with the extensive temporal preprocessing that you are doing and not with the wb_command -cifti-average-roi-correlation command or the CIFTI grayordinates themselves. Is this whole brain data with full coverage of the CIFTI grayordinates space? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Leah Moreno <mmorenoort...@icloud.com> Date: Wednesday, May 17, 2017 at 4:36 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] NaNs and grayordinates with constant timeseries Dear experts, I have run the HCP pipeline w/o errors. However, for a few patients the functional connectivity maps are empty, i.e. the correlation fitting routine does not converge for any region of the brain. The command I use is: wb_command -cifti-average-roi-correlation ${basedir}/${idfolder}/${idfolder}_FCmap_from_seed.dscalar.nii -cifti-roi seed.dscalar.nii –cifti ${basedir}/${idfolder} RS_fMRI_1_Atlas_x4_mov_regr_b_lt_resid_brain_regr_resid_frcintrp_bpss_lc800_hc2.dtseries.nii There are NaNs in the data sometimes. And in the dense timeseries data, there are grayordinates with a constant timeseries. How can I solve this problem? Thank you very much in advance. Best wishes, Leah Moran _______________________________________________ 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