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
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