The ft CIFTI functions are unsupported. Please use the functions located here:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Leonardo Tozzi <[email protected]<mailto:[email protected]>> Date: Friday, August 10, 2018 at 7:25 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Error writing .ptseries file in Matlab To Whom it may concern, I have created a .dlabel.nii file that is a parcellation covering both cortical and subcortical areas. Then, I have extracted mean values for each of the parcels from a contrast map using wb_command -cifti-parcellate. After loading the resulting ptseries.nii files in matlab (using ft_readcifti), I would like to perform some operations on the values stored in the ptseries field, create a new .ptseries.nii file with the new values and visualize it in workbench. Unfortunately, I can’t succeed in saving a CIFTI file that is read by workbench correctly. Given that “cif” is my matlab structure, the output from ft_readcifti, with the values in cif.ptseries changed with the results of my calculations, I have attempted to use ft_write_cifti in several ways: ft_write_cifti('test', cif, 'parameter', 'ptseries', 'brainstructure', 'brainordinate.brainstructure', 'parcellation', 'brainordinate.parcellation') Returns no errors, but then if I try: ft_read_cifti('test.ptseries.nii') Undefined function or variable 'pos'. Error in ft_read_cifti (line 601) brainordinate.brainstructure = zeros(size(pos,1),1); If instead I try: ft_write_cifti('test', cif, 'parameter', 'ptseries') I get a long list of regions: parcel L_Amygdala contains 315 vertices in CIFTI_STRUCTURE_INVALID parcel R_Amygdala contains 332 vertices in CIFTI_STRUCTURE_INVALID parcel L_Hippocampus contains 764 vertices in CIFTI_STRUCTURE_INVALID parcel R_Hippocampus contains 795 vertices in CIFTI_STRUCTURE_INVALID parcel L_Accumbens contains 135 vertices in CIFTI_STRUCTURE_INVALID parcel R_Accumbens contains 140 vertices in CIFTI_STRUCTURE_INVALID parcel L_Caudate contains 728 vertices in CIFTI_STRUCTURE_INVALID parcel R_Caudate contains 755 vertices in CIFTI_STRUCTURE_INVALID parcel L_Pallidum contains 297 vertices in CIFTI_STRUCTURE_INVALID parcel R_Pallidum contains 260 vertices in CIFTI_STRUCTURE_INVALID parcel L_Putamen contains 1060 vertices in CIFTI_STRUCTURE_INVALID parcel R_Putamen contains 1010 vertices in CIFTI_STRUCTURE_INVALID parcel L_Thalamus contains 1288 vertices in CIFTI_STRUCTURE_INVALID parcel R_Thalamus contains 1248 vertices in CIFTI_STRUCTURE_INVALID parcel BrainStem contains 3472 vertices in CIFTI_STRUCTURE_INVALID parcel L_VentralDiencephalon contains 706 vertices in CIFTI_STRUCTURE_INVALID parcel R_VentralDiencephalon contains 712 vertices in CIFTI_STRUCTURE_INVALID parcel L_Cerebellum contains 8709 vertices in CIFTI_STRUCTURE_INVALID parcel R_Cerebellum contains 9144 vertices in CIFTI_STRUCTURE_INVALID parcel R_V1_ROI contains 787 vertices in CIFTI_STRUCTURE_CORTEX_RIGHT parcel R_MST_ROI contains 76 vertices in CIFTI_STRUCTURE_CORTEX_RIGHT (…) The file gets written, but if I try to open it I get: ft_read_cifti('test.ptseries.nii') Dot indexing is not supported for variables of this type. Error in ft_read_cifti (line 439) sel = strcmp({Surface(:).BrainStructure}, Parcel(j).BrainStructure{k}); Workbench also will not open the files generated this way, with two kinds of errors: for the first file: “xml and nifti header disagree on matrix dimensions” and for the second one: “Cifti XML error: you must set surfaces before adding parcels that use them”. I suspect I am either missing something basic in the syntax of ft_write_cifti or my original .ptseries.nii files have something strange about them. Thank you very much. Yours faithfully, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd [email protected]<mailto:[email protected]> | (650) 5615738 _______________________________________________ HCP-Users mailing list [email protected]<mailto:[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. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
