I am guessing that somehow the medial wall ROIs did not get used in the PALM analysis. Perhaps Anderson can help us understand how that could have happened. It would probably help to give the command lines you used with PALM.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of JOANA LOUREIRO <jloure...@ucla.edu<mailto:jloure...@ucla.edu>> Date: Thursday, September 20, 2018 at 4:49 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] beta extraction from ROI using cifti data - ERROR: roi cifti does not match input cifti along columns We are an HCP diseased connectome site. I used PALM to compute group differences between patients and controls at baseline. After using -cifti-find-clsters on the fwep maps obtained from palm. I multiplied the obtained cluster map with a structural mask of of the amygdala. The resulting ROI (combined functional and structural mask) is then used to extract beta values on a longitudinal analysis on the patients (with three time points: before treatment, after treatment and 3 months after treatment). After preforming the PALM analysis and obtaining the combined ROI for each subject I was trying to use -cifti-stats to extract the beta values for each subject. However I am getting an error : ERROR: roi cifti does not match input cifti along columns Here the command I used: wb_command -cifti-stats ${sub}/MNINonLinear/Results/task-facematching_level2/task-facematching_hp200_s5_level2.feat/${sub}_task-facematching_level2_beta_HAPPY_hp200_s5.dscalar.nii -reduce MEAN -roi ${sub}-combinedmask_AMYGDALA-RIGHT_clusters-cope10.dscalar.nii -match-maps This error comes not only with this command but also with -cifti-weighted-stats or -cifti-average-dense-rois when getting the information of each file (info bellow) the only thing I find different is in the row that says CORTEX LEFT and CORTEX RIGHT (underlined in yellow). Is that the problem? did I do something wrong? How do you suggest I go around this problem? thanks a lot for the help, Joana Loureiro #FILE INFORMATION for: ${sub}_task-facematching_level2_beta_HAPPY_hp200_s5.dscalar.nii ############################################### Name: k000801_task-facematching_level2_beta_HAPPY_hp200_s5.dscalar.nii Type: Connectivity - Dense Scalar Structure: CortexLeft CortexRight Data Size: 365.13 Kilobytes Maps to Surface: true Maps to Volume: true 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: 91282 Number of Columns: 1 Volume Dim[0]: 91 Volume Dim[1]: 109 Volume Dim[2]: 91 Palette Type: Map (Unique for each map) CIFTI Dim[0]: 1 CIFTI Dim[1]: 91282 ALONG_ROW map type: SCALARS ALONG_COLUMN map type: BRAIN_MODELS Has Volume Data: true Volume Dims: 91,109,91 Volume Space: -2,0,0,90;0,2,0,-126;0,0,2,-72 CortexLeft: 29696 out of 32492 vertices CortexRight: 29716 out of 32492 vertices AccumbensLeft: 135 voxels AccumbensRight: 140 voxels AmygdalaLeft: 315 voxels AmygdalaRight: 332 voxels BrainStem: 3472 voxels CaudateLeft: 728 voxels CaudateRight: 755 voxels CerebellumLeft: 8709 voxels CerebellumRight: 9144 voxels DiencephalonVentralLeft: 706 voxels DiencephalonVentralRight: 712 voxels HippocampusLeft: 764 voxels HippocampusRight: 795 voxels PallidumLeft: 297 voxels PallidumRight: 260 voxels PutamenLeft: 1060 voxels PutamenRight: 1010 voxels ThalamusLeft: 1288 voxels ThalamusRight: 1248 voxels Map Minimum Maximum Mean Sample Dev % Positive % Negative Inf/NaN Map Name 1 -8.370 4.024 -2.272 1.339 4.848 95.152 0 k000801_task-facematching_level2_FEARFUL-HAPPY_hp200_s5 #FILE INFORMATION for: ${sub}-combinedmask_AMYGDALA_RIGHT_clusters-cope10.dscalar.nii########################################## Name: k000801-combinedmask_AMYGDALA_RIGHT_clusters-cope10.dscalar.nii Type: Connectivity - Dense Scalar Structure: CortexLeft CortexRight Data Size: 387.42 Kilobytes Maps to Surface: true Maps to Volume: true 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: 96854 Number of Columns: 1 Volume Dim[0]: 91 Volume Dim[1]: 109 Volume Dim[2]: 91 Palette Type: Map (Unique for each map) CIFTI Dim[0]: 1 CIFTI Dim[1]: 96854 ALONG_ROW map type: SCALARS ALONG_COLUMN map type: BRAIN_MODELS Has Volume Data: true Volume Dims: 91,109,91 Volume Space: -2,0,0,90;0,2,0,-126;0,0,2,-72 CortexLeft: 32492 out of 32492 vertices CortexRight: 32492 out of 32492 vertices AccumbensLeft: 135 voxels AccumbensRight: 140 voxels AmygdalaLeft: 315 voxels AmygdalaRight: 332 voxels BrainStem: 3472 voxels CaudateLeft: 728 voxels CaudateRight: 755 voxels CerebellumLeft: 8709 voxels CerebellumRight: 9144 voxels DiencephalonVentralLeft: 706 voxels DiencephalonVentralRight: 712 voxels HippocampusLeft: 764 voxels HippocampusRight: 795 voxels PallidumLeft: 297 voxels PallidumRight: 260 voxels PutamenLeft: 1060 voxels PutamenRight: 1010 voxels ThalamusLeft: 1288 voxels ThalamusRight: 1248 voxels Map Minimum Maximum Mean Sample Dev % Positive % Negative Inf/NaN Map Name 1 0.000 6.000 0.003 0.094 0.199 0.000 0 sub-k000801_L_aparc _______________________________________________ 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. 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