Hi all:
I have three groups of subjects (major depression disorder,slight
depression disorder and contrast),i want to use qdec to obtain the statistical
significant areas containing difference of cortical thickness measurment among
them. But there are some errors appearing when i run the group analysis:
ERROR: QdecGlmDesign::GenerateContrasts: factor 2 must have 2 levels
I think the error is related to the diagnosis.levels file which has 3
levels because i can run it successfully after removing any one of them.But i
don't know why.
Can you give me some help or suggestions?
I have saved error information into the error.log file(see attachments)
HP
MD
DX
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Loading data table qdec.table.dat...
Number of columns: 4
fsid column: 1
Number of factors: 3
Number of subjects: 59
Reading discrete factor levels from config file ./sex.levels
'Male','Female', done
Reading discrete factor levels from config file ./diagnosis.levels
'HP','MD','DX', done
Data table qdec.table.dat loaded.
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n001_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d20' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n003_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd01' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n004_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d02' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n005_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd07' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n009_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd30' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n011_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd15' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n012_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_19' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n013_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d21' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n014_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d28' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n015_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d22' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n016_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d10' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n017_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d11' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n019_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d16' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n020_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd04' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n021_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d14' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n022_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd24' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n023_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d27' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n051_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d25' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n054_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd17' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n008_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_dd05' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'HP_n010_3_a' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'MD_d31' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx19-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx15-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx09-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx16-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx01-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx11-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx06-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx10-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx13-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx08-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx14-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx18-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx07-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx05-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx02-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx03-3D' in
SUBJECTS_DIR
sh: Syntax error: Bad fd number
ERROR: QdecProject::VerifySubjects: Couldn't find subject 'dx12-3D' in
SUBJECTS_DIR
Input table: qdec.table.dat
Subject #, Subject ID, Factor Data...
0 HP_n001_3_a Male 33.000000 HP
1 MD_d20 Male 36.000000 MD
2 HP_n003_3_a Male 30.000000 HP
3 MD_dd01 Male 28.000000 MD
4 HP_n004_3_a Male 23.000000 HP
5 MD_d02 Male 23.000000 MD
6 HP_n005_3_a Male 24.000000 HP
7 MD_dd07 Male 24.000000 MD
8 HP_n009_3_a Male 19.000000 HP
9 MD_dd30 Male 22.000000 MD
10 HP_n011_3_a Female 26.000000 HP
11 MD_dd15 Female 26.000000 MD
12 HP_n012_3_a Female 28.000000 HP
13 MD_19 Female 35.000000 MD
14 HP_n013_3_a Female 23.000000 HP
15 MD_d21 Female 24.000000 MD
16 HP_n014_3_a Male 32.000000 HP
17 MD_d28 Male 27.000000 MD
18 HP_n015_3_a Female 23.000000 HP
19 MD_d22 Female 24.000000 MD
20 HP_n016_3_a Female 21.000000 HP
21 MD_d10 Female 19.000000 MD
22 HP_n017_3_a Female 21.000000 HP
23 MD_d11 Female 21.000000 MD
24 HP_n019_3_a Female 25.000000 HP
25 MD_d16 Female 20.000000 MD
26 HP_n020_3_a Male 23.000000 HP
27 MD_dd04 Male 25.000000 MD
28 HP_n021_3_a Female 19.000000 HP
29 MD_d14 Female 19.000000 MD
30 HP_n022_3_a Male 23.000000 HP
31 MD_dd24 Male 23.000000 MD
32 HP_n023_3_a Male 23.000000 HP
33 MD_d27 Male 24.000000 MD
34 HP_n051_3_a Female 19.000000 HP
35 MD_d25 Female 19.000000 MD
36 HP_n054_3_a Female 18.000000 HP
37 MD_dd17 Female 18.000000 MD
38 HP_n008_3_a Male 19.000000 HP
39 MD_dd05 Male 21.000000 MD
40 HP_n010_3_a Female 28.000000 HP
41 MD_d31 Female 26.000000 DX
42 dx19-3D Male 20.000000 DX
43 dx15-3D Female 29.000000 DX
44 dx09-3D Male 18.000000 DX
45 dx16-3D Female 43.000000 DX
46 dx01-3D Male 21.000000 DX
47 dx11-3D Female 26.000000 DX
48 dx06-3D Male 18.000000 DX
49 dx10-3D Male 26.000000 DX
50 dx13-3D Female 38.000000 DX
51 dx08-3D Male 32.000000 DX
52 dx14-3D Male 37.000000 DX
53 dx18-3D Female 31.000000 DX
54 dx07-3D Male 21.000000 DX
55 dx05-3D Female 21.000000 DX
56 dx02-3D Female 19.000000 DX
57 dx03-3D Male 22.000000 DX
58 dx12-3D Male 32.000000 DX
1 sex discrete 2
1 Male
2 Female
2 age continuous 0
3 diagnosis discrete 3
1 HP
2 MD
3 DX
Continuous Factors: Mean: StdDev:
------------------- ----- -------
age 24.712 5.690
Number of subjects: 59
Number of factors: 3 (2 discrete, 1 continuous)
Number of classes: 6
Number of regressors: 12
============================================================
SUBJECTS_DIR is '/mnt/F_data/Data_MDD/processed_data'
ERROR: QdecGlmDesign::GenerateContrasts: factor 2 must have 2 levels
ninputs = 59
Checking inputs
nframestot = 59
Allocing output
nframes = 59
Writing to /mnt/F_data/Data_MDD/processed_data/qdec/Untitled/y.mgh
gdfReadHeader: reading
/mnt/F_data/Data_MDD/processed_data/qdec/Untitled/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 age 24.7119
Class Means of each Continuous Variable
1 sexMale-diagnosisHP 24.9000
2 sexFemale-diagnosisHP 22.8182
3 sexMale-diagnosisMD 25.3000
4 sexFemale-diagnosisMD 22.5000
5 sexMale-diagnosisDX 24.7000
6 sexFemale-diagnosisDX 29.1250
INFO: gd2mtx_method is dods
Reading source surface
/mnt/F_data/Data_MDD/processed_data/fsaverage/surf/lh.white
reading group avg surface area 822 cm^2 from file
Reading in average area
/mnt/F_data/Data_MDD/processed_data/fsaverage/surf/lh.white.avg.area.mgh
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y
/mnt/F_data/Data_MDD/processed_data/qdec/Untitled/y.mgh --fsgd
/mnt/F_data/Data_MDD/processed_data/qdec/Untitled/qdec.fsgd dods --glmdir
/mnt/F_data/Data_MDD/processed_data/qdec/Untitled --surf fsaverage lh --label
/mnt/F_data/Data_MDD/processed_data/fsaverage/label/lh.cortex.label subjid sex age diagnosis
HP_n001_3_a Male 33.000000 HP
MD_d20 Male 36.000000 MD
HP_n003_3_a Male 30.000000 HP
MD_dd01 Male 28.000000 MD
HP_n004_3_a Male 23.000000 HP
MD_d02 Male 23.000000 MD
HP_n005_3_a Male 24.000000 HP
MD_dd07 Male 24.000000 MD
HP_n009_3_a Male 19.000000 HP
MD_dd30 Male 22.000000 MD
HP_n011_3_a Female 26.000000 HP
MD_dd15 Female 26.000000 MD
HP_n012_3_a Female 28.000000 HP
MD_19 Female 35.000000 MD
HP_n013_3_a Female 23.000000 HP
MD_d21 Female 24.000000 MD
HP_n014_3_a Male 32.000000 HP
MD_d28 Male 27.000000 MD
HP_n015_3_a Female 23.000000 HP
MD_d22 Female 24.000000 MD
HP_n016_3_a Female 21.000000 HP
MD_d10 Female 19.000000 MD
HP_n017_3_a Female 21.000000 HP
MD_d11 Female 21.000000 MD
HP_n019_3_a Female 25.000000 HP
MD_d16 Female 20.000000 MD
HP_n020_3_a Male 23.000000 HP
MD_dd04 Male 25.000000 MD
HP_n021_3_a Female 19.000000 HP
MD_d14 Female 19.000000 MD
HP_n022_3_a Male 23.000000 HP
MD_dd24 Male 23.000000 MD
HP_n023_3_a Male 23.000000 HP
MD_d27 Male 24.000000 MD
HP_n051_3_a Female 19.000000 HP
MD_d25 Female 19.000000 MD
HP_n054_3_a Female 18.000000 HP
MD_dd17 Female 18.000000 MD
HP_n008_3_a Male 19.000000 HP
MD_dd05 Male 21.000000 MD
HP_n010_3_a Female 28.000000 HP
MD_d31 Female 26.000000 DX
dx19-3D Male 20.000000 DX
dx15-3D Female 29.000000 DX
dx09-3D Male 18.000000 DX
dx16-3D Female 43.000000 DX
dx01-3D Male 21.000000 DX
dx11-3D Female 26.000000 DX
dx06-3D Male 18.000000 DX
dx10-3D Male 26.000000 DX
dx13-3D Female 38.000000 DX
dx08-3D Male 32.000000 DX
dx14-3D Male 37.000000 DX
dx18-3D Female 31.000000 DX
dx07-3D Male 21.000000 DX
dx05-3D Female 21.000000 DX
dx02-3D Female 19.000000 DX
dx03-3D Male 22.000000 DX
dx12-3D Male 32.000000 DX
Male
Female
HP_n001_3_a
MD_d20
HP_n003_3_a
MD_dd01
HP_n004_3_a
MD_d02
HP_n005_3_a
MD_dd07
HP_n009_3_a
MD_dd30
HP_n011_3_a
MD_dd15
HP_n012_3_a
MD_19
HP_n013_3_a
MD_d21
HP_n014_3_a
MD_d28
HP_n015_3_a
MD_d22
HP_n016_3_a
MD_d10
HP_n017_3_a
MD_d11
HP_n019_3_a
MD_d16
HP_n020_3_a
MD_dd04
HP_n021_3_a
MD_d14
HP_n022_3_a
MD_dd24
HP_n023_3_a
MD_d27
HP_n051_3_a
MD_d25
HP_n054_3_a
MD_dd17
HP_n008_3_a
MD_dd05
HP_n010_3_a
MD_d31
dx19-3D
dx15-3D
dx09-3D
dx16-3D
dx01-3D
dx11-3D
dx06-3D
dx10-3D
dx13-3D
dx08-3D
dx14-3D
dx18-3D
dx07-3D
dx05-3D
dx02-3D
dx03-3D
dx12-3D
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