There are NaNs in the STDEV map? That suggests your earlier temporal processing introduced them. You would need to go through each step of that and find where they are coming from.
Peace, Matt. From: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Wednesday, April 19, 2017 at 9:54 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file Dear Matt, I have used wb_command -cifti-reduce STDEV to assess dense timeseries data and there are NANs. Please advise. Thank you very much, -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, April 18, 2017 at 9:06 AM To: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file What about in the dense timeseries data? Are there grayordinates with a constant timeseries? You could use wb_command -cifti-reduce STDEV to assess. Peace, Matt. From: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Tuesday, April 18, 2017 at 8:01 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file Yes, there are NANs. What should I do next? Thanks again, -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Tuesday, April 18, 2017 at 7:58 AM To: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file Are there NaNs in the data sometimes after all of that heavy temporal preprocessing? Peace, Matt. From: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Monday, April 17, 2017 at 11:37 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file wb_command -cifti-average-roi-correlation ${basedir}/${idfolder}/${idfolder}_FCmap_from_seed.dscalar.nii -cifti-roi seed.dscalar.nii –cifti RS_fMRI_1_Atlas_x4_mov_regr_b_lt_resid_brain_regr_resid_frcintrp_bpss_lc800_hc2.dtseries.nii The same command works for some dtseries.nii but not for others from which I am getting an empty FCmap. I did not get an error running the HCP pipeline in any step, and the dtseries.nii looks fine to me using wb_view. Please advise. Thanks a lot, -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Monday, April 17, 2017 at 10:06 PM To: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file How are you calling the command? Peace, Matt. From: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Sunday, April 16, 2017 at 9:11 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file Dear Matt, Thank you very much. I save it with the ciftisavereset function. But still I am getting an empty functional connectivity map when running wb_command -cifti-average-roi-correlation on my final dtseries.nii. I have loaded final dtseries.nii in wb_view and it looks good. Do you know what might be wrong? -L From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Sunday, April 16, 2017 at 2:01 PM To: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] change dimensions in a cifti file This is what the ciftisavereset function is for (which should be available in the same place you found ciftiopen and ciftisave. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Sunday, April 16, 2017 at 12:31 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] change dimensions in a cifti file Dear experts, I want to convert from nii to cii, and I am using wb_command -cifti-convert -from-nifti What is the best way to change dimensions in a cifti file to use as the template? (e.g., from 91282x236 to 91282x127) I am doing: cii = ciftiopen('RS_fMRI_1_Atlas.dtseries.nii','/usr/local/workbench/bin_macosx64/wb_command') cii = cdata: [91282x236 single] cii.cdata=cii.cdata(:,1:127) cii = cdata: [91282x127 single] newcii = cii; ciftisave(newcii,'RS_fMRI_1_template.dtseries.nii','/usr/local/workbench/bin_macosx64/wb_command') But when running wb_command -cifti-average-roi-correlation on my final dtseries.nii file the map is empty. Any idea what is going on? Thank you very much in advance -L _______________________________________________ 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. 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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
