You can use -cifti-parcellate with the -method option to get the desired type of statistic, and then use -cifti-convert -to-text to turn it into a tab delimited or csv file.
Tim On Sun, Apr 16, 2017 at 9:32 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > I guess that doesn’t work either. We’ll have to wait for Tim to provide > more suggestions… > > Peace, > > Matt. > > From: stargazy pie <1257735...@qq.com> > Date: Sunday, April 16, 2017 at 9:30 AM > To: Matt Glasser <glass...@wustl.edu> > Subject: 回复： 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, > ./wb_command -cifti-parcellate /home/Tianjie/projects/WU- > Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/ > MNINonLinear/fsaverage_LR32k/LS2001.MyelinMap.32k_fs_LR.dscalar.nii > /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_ > structure_preprocess/LS2001/MNINonLinear/fsaverage_LR32k/ > LS2001.aparc.32k_fs_LR.dlabel.nii COLUMN LS2001_average_myelin.pscalar.nii > > ./wb_command -file-information /home/Tianjie/connectome_ > workbench/workbench/bin_rh_linux64/LS2001_average_myelin.pscalar.nii > Name: /home/Tianjie/connectome_ > workbench/workbench/bin_rh_linux64/LS2001_average_myelin.pscalar.nii > Type: Connectivity - Parcel Scalar > Structure: CortexLeft CortexRight > Data Size: 272.00 Bytes > Maps to Surface: true > Maps to Volume: false > Maps with LabelTable: false > Maps with Palette: true > All Map Palettes Equal: true > Map Interval Units: NIFTI_UNITS_UNKNOWN > Number of Maps: 1 > Number of Rows: 68 > Number of Columns: 1 > Volume Dim[0]: 0 > Volume Dim[1]: 0 > Volume Dim[2]: 0 > Palette Type: Map (Unique for each map) > CIFTI Dim[0]: 1 > CIFTI Dim[1]: 68 > ALONG_ROW map type: SCALARS > ALONG_COLUMN map type: PARCELS > Has Volume Data: false > CortexLeft: 32492 vertices > CortexRight: 32492 vertices > Parcel 1: L_bankssts > CortexLeft: 462 vertices > Parcel 2: L_caudalanteriorcingulate > CortexLeft: 219 vertices > Parcel 3: L_caudalmiddlefrontal > CortexLeft: 750 vertices > Parcel 4: L_cuneus > CortexLeft: 330 vertices > Parcel 5: L_entorhinal > CortexLeft: 157 vertices > Parcel 6: L_fusiform > CortexLeft: 876 vertices > Parcel 7: L_inferiorparietal > CortexLeft: 1785 vertices > Parcel 8: L_inferiortemporal > CortexLeft: 875 vertices > Parcel 9: L_isthmuscingulate > CortexLeft: 381 vertices > Parcel 10: L_lateraloccipital > CortexLeft: 1234 vertices > Parcel 11: L_lateralorbitofrontal > CortexLeft: 817 vertices > Parcel 12: L_lingual > CortexLeft: 823 vertices > Parcel 13: L_medialorbitofrontal > CortexLeft: 485 vertices > Parcel 14: L_middletemporal > CortexLeft: 904 vertices > Parcel 15: L_parahippocampal > CortexLeft: 263 vertices > Parcel 16: L_paracentral > CortexLeft: 687 vertices > Parcel 17: L_parsopercularis > CortexLeft: 604 vertices > Parcel 18: L_parsorbitalis > CortexLeft: 170 vertices > Parcel 19: L_parstriangularis > CortexLeft: 410 vertices > Parcel 20: L_pericalcarine > CortexLeft: 371 vertices > Parcel 21: L_postcentral > CortexLeft: 1903 vertices > Parcel 22: L_posteriorcingulate > CortexLeft: 525 vertices > Parcel 23: L_precentral > CortexLeft: 2111 vertices > Parcel 24: L_precuneus > CortexLeft: 1501 vertices > Parcel 25: L_rostralanteriorcingulate > CortexLeft: 206 vertices > Parcel 26: L_rostralmiddlefrontal > CortexLeft: 1433 vertices > Parcel 27: L_superiorfrontal > CortexLeft: 2486 vertices > Parcel 28: L_superiorparietal > CortexLeft: 2053 vertices > Parcel 29: L_superiortemporal > CortexLeft: 1410 vertices > Parcel 30: L_supramarginal > CortexLeft: 1553 vertices > Parcel 31: L_frontalpole > CortexLeft: 72 vertices > Parcel 32: L_temporalpole > CortexLeft: 166 vertices > Parcel 33: L_transversetemporal > CortexLeft: 185 vertices > Parcel 34: L_insula > CortexLeft: 1100 vertices > Parcel 35: R_bankssts > CortexRight: 367 vertices > Parcel 36: R_caudalanteriorcingulate > CortexRight: 217 vertices > Parcel 37: R_caudalmiddlefrontal > CortexRight: 738 vertices > Parcel 38: R_cuneus > CortexRight: 332 vertices > Parcel 39: R_entorhinal > CortexRight: 166 vertices > Parcel 40: R_fusiform > CortexRight: 924 vertices > Parcel 41: R_inferiorparietal > CortexRight: 1748 vertices > Parcel 42: R_inferiortemporal > CortexRight: 840 vertices > Parcel 43: R_isthmuscingulate > CortexRight: 390 vertices > Parcel 44: R_lateraloccipital > CortexRight: 1131 vertices > Parcel 45: R_lateralorbitofrontal > CortexRight: 850 vertices > Parcel 46: R_lingual > CortexRight: 853 vertices > Parcel 47: R_medialorbitofrontal > CortexRight: 517 vertices > Parcel 48: R_middletemporal > CortexRight: 971 vertices > Parcel 49: R_parahippocampal > CortexRight: 296 vertices > Parcel 50: R_paracentral > CortexRight: 764 vertices > Parcel 51: R_parsopercularis > CortexRight: 509 vertices > Parcel 52: R_parsorbitalis > CortexRight: 209 vertices > Parcel 53: R_parstriangularis > CortexRight: 489 vertices > Parcel 54: R_pericalcarine > CortexRight: 344 vertices > Parcel 55: R_postcentral > CortexRight: 1848 vertices > Parcel 56: R_posteriorcingulate > CortexRight: 515 vertices > Parcel 57: R_precentral > CortexRight: 2074 vertices > Parcel 58: R_precuneus > CortexRight: 1489 vertices > Parcel 59: R_rostralanteriorcingulate > CortexRight: 176 vertices > Parcel 60: R_rostralmiddlefrontal > CortexRight: 1508 vertices > Parcel 61: R_superiorfrontal > CortexRight: 2311 vertices > Parcel 62: R_superiorparietal > CortexRight: 2052 vertices > Parcel 63: R_superiortemporal > CortexRight: 1385 vertices > Parcel 64: R_supramarginal > CortexRight: 1817 vertices > Parcel 65: R_frontalpole > CortexRight: 58 vertices > Parcel 66: R_temporalpole > CortexRight: 182 vertices > Parcel 67: R_transversetemporal > CortexRight: 153 vertices > Parcel 68: R_insula > CortexRight: 1092 vertices > > Map Minimum Maximum Mean Sample Dev % Positive % Negative > Inf/NaN Map Name > 1 1.240 1.797 1.468 0.116 100.000 0.000 > 0 LS2001_MyelinMap > > Maybe, I need -spatial-weights flag? Where can I find corresponding > weights file? > Thanks. > > > ------------------ 原始邮件 ------------------ > *发件人:* "Glasser, Matthew";<glass...@wustl.edu>; > *发送时间:* 2017年4月16日(星期天) 晚上10:05 > *收件人:* "stargazy pie"<1257735...@qq.com>; "hcp-users@humanconnectome.org"< > hcp-users@humanconnectome.org>; > *主题:* Re: 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 > > 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 <1257735...@qq.com> > Date: Sunday, April 16, 2017 at 8:57 AM > To: Matt Glasser <glass...@wustl.edu> > 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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月16日 21:19 > *收件人:* stargazy pie <1257735...@qq.com>; hcp-users@humanconnectome.org > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 11:27 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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";<glass...@wustl.edu>; > > *发送时间**:* 2017年4月16日(星期天) 中午12:03 > > *收件人**:* "stargazy pie"<1257735...@qq.com>; "hcp-users@humanconnectome.org > "<hcp-users@humanconnectome.org>; > > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 10:33 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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"<glass...@wustl.edu> > > *发送时间**:* 2017年4月16日 11:18:32 > > *收件人**:* "hcp-users@humanconnectome.org"<hcp-users@humanconnectome.org > >;"wtj"<1257735...@qq.com>; > > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 9:38 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月16日 10:34 > *收件人:* wtj <1257735...@qq.com>; hcp-users@humanconnectome.org > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 9:25 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月16日 9:53 > *收件人:* wtj <1257735...@qq.com>; hcp-users@humanconnectome.org > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 8:28 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月16日 9:11 > *收件人:* wtj <1257735...@qq.com>; hcp-users@humanconnectome.org > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 7:59 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月16日 8:39 > *收件人:* wtj <1257735...@qq.com>; hcp-users@humanconnectome.org > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 7:37 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月16日 8:02 > *收件人:* wtj <1257735...@qq.com>; hcp-users@humanconnectome.org > *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 <1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 6:32 PM > *To: *Matt Glasser <glass...@wustl.edu> > *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:glass...@wustl.edu <glass...@wustl.edu>] > *发送时间:* 2017年4月15日 22:25 > *收件人:* wtj <1257735...@qq.com>; hcp-users@humanconnectome.org > *主题:* Re: [HCP-Users] myelin maps > > > > You have put the myelin map where the ROI should go. > > > > Peace, > > > > Matt. > > > > *From: *<hcp-users-boun...@humanconnectome.org> on behalf of wtj < > 1257735...@qq.com> > *Date: *Saturday, April 15, 2017 at 9:22 AM > *To: *"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > *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? > > Thanks. > > _______________________________________________ > HCP-Users mailing list > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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. > > > ------------------------------ > > 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
