Thanks Matt and Tim for your answers. The -cifti-parcellate command seems to be just what I needed and working fine with the aparc file. I'll have a look at this new parcellation though, that looks interesting!
Best, JF De : Glasser, Matthew [mailto:glass...@wustl.edu] Envoyé : 12 octobre 2016 20:19 À : NEUROSCIENCE tim <tsc...@mst.edu>; Jean-Francois Cabana <jfcab...@outlook.com> Cc : hcp-users@humanconnectome.org Objet : Re: [HCP-Users] get ROIs average The aparc file is indeed a surface only file. This is not a recommended cortical parcellation. I recommend you use this one: https://balsa.wustl.edu/study/show/RVVG Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Wednesday, October 12, 2016 at 3:08 PM To: Jean-Francois Cabana <jfcab...@outlook.com<mailto:jfcab...@outlook.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] get ROIs average That error actually means that the grayordinate space isn't the same - either there is no volume data in one of them, or medial wall masks weren't used, or the ROIs were different, or... I'm not familiar with a dlabel form of the aparc file, but as the filename suggests that it is surface-based for cortex, you should be able to use -cifti-parcellate to do what you want, followed by -cifti-convert -to-text to get it as a text form. The output of -cifti-parcellate is a parcellated cifti file, which also contains the metadata required to display the area averages as patches of color on the surfaces (and in volume if there are volume parcels). The -cifti-parcellate command is a bit more forgiving in that it should work as long as the surface resolution and volume space (if the dlabel has volume data) are matched up. Note that if the dlabel file does not distinguish between left and right labels, then the parcellated output for areas will be averaged across both hemispheres. Tim On Wed, Oct 12, 2016 at 7:19 AM, Jean-Francois Cabana <jfcab...@outlook.com<mailto:jfcab...@outlook.com>> wrote: Dear HCP users, I'm trying to find out how to compute ROIs average from a dscalar file. What I want to do is take all ROIs from the aparc.dlabel.nii file and compute the average from a dscalar.nii file in each label and print the values to a text file. What I did was first to convert the labels to ROIs with the -cifti-all-labels-to-rois command, and then use the resulting roi file in the -cifti-roi-average command. For example : wb_command -cifti-all-labels-to-rois HN82.aparc.164k_fs_LR.dlabel.nii 1 HN82.aparc.roi.164k_fs_LR.dscalar.nii wb_command -cifti-roi-average HN82.DKI_mk.164k_fs_LR.dscalar.nii HN82.DKI_mk.txt -cifti-roi HN82.aparc.roi.164k_fs_LR.dscalar.nii But then I get this error : ERROR: dense mappings of input and roi cifti files don't match I think the problem might be that the ROI file contains several maps, one for each ROI, while the dscalar has only one. Is there a way to do what I want to do without having for example to split the ROI in several files, one for each label? Thanks in advance, JF _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ 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. 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
