No you would need to run wb_command -cifti-parcellate to make a .pscalar.nii from the myelin map .dscalar.nii and then wb_command -file-information to get the means per area.
Peace, Matt. From: wtj <[email protected]<mailto:[email protected]>> Date: Sunday, April 16, 2017 at 8:57 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: 答复: [SPAM] 回复： [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, What is “MEAN” column in the table? Is it what I need? It says Type is Connectivity-Dense Scalar, what does “Connectivity” mean? Thanks. 发件人: Glasser, Matthew [mailto:[email protected]] 发送时间: 2017年4月16日 21:19 收件人: stargazy pie <[email protected]<mailto:[email protected]>>; [email protected]<mailto:[email protected]> 主题: Re: [SPAM] 回复： [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 I would have thought that this would list values for all ROIs (if there are multiple maps in the ROI file) so we’ll have to wait for Tim Coalson to comment. Peace, Matt. From: stargazy pie <[email protected]<mailto:[email protected]>> Date: Saturday, April 15, 2017 at 11:27 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Subject: [SPAM] 回复： [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, This is what it looks like: [root@localhost bin_rh_linux64]# ./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 1.441055 [root@localhost bin_rh_linux64]# 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(星期天) 中午12:03 收件人: "stargazy pie"<[email protected]<mailto:[email protected]>>; "[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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