Indeed it looks like we need to make this easier for folks to do as those e-mails suggest there isn’t currently a way to do this. As I said in a previous e-mail, you can probably use wb_command -cifti-parcellate and then wb_command -file-information on the .pscalar.nii file to get means.
Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Sunday, April 16, 2017 at 1:28 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: 答复: [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, https://www.mail-archive.com/[email protected]/msg03582.html If you are still confused, my question is just like what Timothy Hendrickson said. The most important thing is, objectively, can I get a subject’s myelin value of different brain regions? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 12:03 收件人: stargazy pie <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps How about pasting it in to the e-mail. Peace, Matt. From: stargazy pie <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 10:33 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 回复：[SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, It is just a float number following the -cifti-stats command. I don't know, but, will there be other output file anywhere else? Thanks. ---原始邮件--- 发件人: "Glasser, Matthew"<[email protected]<mailto:[email protected]>> 发送时间: 2017年4月16日 11:18:32 收件人: "[email protected]<mailto:[email protected]>"<[email protected]<mailto:[email protected]>>;"wtj"<[email protected]<mailto:[email protected]>>; 主题: Re: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps What is the output of your wb_command -cifti-stats command? Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 9:38 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, What I mean is, every region of brain have different average thickness, at the same time, they should also have different myelin values. This is what I want. Sorry to bother you so late… Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 10:34 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps What is it that you want? Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 9:25 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, After extracting ROIs using wb_command –cifti-all-labels-to-rois, I got a table, with each ROI, I got the ROI’s minimum, maximum, mean, et al. I use this file : ./wb_command -cifti-all-labels-to-rois /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/fsaverage_LR32k/LS2001.aparc.32k_fs_LR.dlabel.nii 1 mycommandlabeltoroi.dscalar.nii ./wb_command -cifti-stats /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/fsaverage_LR32k/LS2001.MyelinMap.32k_fs_LR.dscalar.nii -roi /home/Tianjie/connectome_workbench/workbench/bin_rh_linux64/mycommandlabeltoroi.dscalar.nii -reduce MEAN The result is still just a number. Maybe , I sould use a file of only one ROI at a time? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 9:53 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps A dlabel.nii parcellation is not an ROI, but a set of them. You can extract ROIs using wb_command -cifti-all-labels-to-rois or -cifti-label-to-roi. Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 8:28 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, Do you mean that I used wrong ROI file, or ROI file is not produced yet? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 9:11 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Perhaps you need a combination of wb_command -cifti-parcellate and wb_command -file-information. Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 7:59 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 答复: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, What does –reduce flag mean in wb_command –cifti-stats? When I used –reduce MEAN, it only outputed one number. I need myelin values of every ROI. What should I do? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 8:39 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Perhaps you should be using wb_command -cifti-stats if you don’t want to provide weights. Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 7:37 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 答复: [SPAM] 答复: [HCP-Users] myelin maps Hi, This is what I do: ./wb_command -cifti-weighted-stats /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/fsaverage_LR32k/LS2001.MyelinMap.32k_fs_LR.dscalar.nii -roi /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/fsaverage_LR32k/LS2001.aparc.32k_fs_LR.dlabel.nii ERROR: you must use exactly one of –spatial-weights or –cifti-weights. If I use the latter, what will the weights file’s name be like? Where can I find it? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 8:02 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 答复: [HCP-Users] myelin maps You need to use appropriate files for the CIFTI and ROI arguments. Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 6:32 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 答复: [HCP-Users] myelin maps Hi, There is another error when I exchanged the position of –roi flag and the myelin map file. ERROR: roi-cifti is missing(No more parameters). Should I add something else? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月15日 22:25 收件人: wtj <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [HCP-Users] myelin maps You have put the myelin map where the ROI should go. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of wtj <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 9:22 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] myelin maps Hi, I know someone has asked in mail list about extracting average myelin value at ROI level. My command is: ./wb_command –cifti-weighted-stats –roi ./LS2001/MNINonLinear/LS2001.MyelinMap.164k_fs_LR.dscalar.nii Error: cifti-in is missing(No more parameters). How to fix the error? 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