Thank you for your response.
I tried the link which you sent yesterday. But got stuck while creating qdec.fsgd file.
Below i have pasted the terminal output after loading the data.
1 Left-Lateral-Ventricle continuous 0
2 Left-Inf-Lat-Vent continuous 0
3 Left-Cerebellum-White-Matter continuous 0
4 Left-Cerebellum-Cortex continuous 0
5 Left-Thalamus-Proper continuous 0
6 Left-Caudate continuous 0
7 Left-Putamen continuous 0
8 Left-Pallidum continuous 0
9 3rd-Ventricle continuous 0
10 4th-Ventricle continuous 0
11 Brain-Stem continuous 0
12 Left-Hippocampus continuous 0
13 Left-Amygdala continuous 0
14 CSF continuous 0
15 Left-Accumbens-area continuous 0
16 Left-VentralDC continuous 0
17 Left-vessel continuous 0
18 Left-choroid-plexus continuous 0
19 Right-Lateral-Ventricle continuous 0
20 Right-Inf-Lat-Vent continuous 0
21 Right-Cerebellum-White-Matter continuous 0
22 Right-Cerebellum-Cortex continuous 0
23 Right-Thalamus-Proper continuous 0
24 Right-Caudate continuous 0
25 Right-Putamen continuous 0
26 Right-Pallidum continuous 0
27 Right-Hippocampus continuous 0
28 Right-Amygdala continuous 0
29 Right-Accumbens-area continuous 0
30 Right-VentralDC continuous 0
31 Right-vessel continuous 0
32 Right-choroid-plexus continuous 0
33 WM-hypointensities continuous 0
34 Optic-Chiasm continuous 0
35 CC_Posterior continuous 0
36 CC_Mid_Posterior continuous 0
37 CC_Central continuous 0
38 CC_Mid_Anterior continuous 0
39 CC_Anterior continuous 0
40 diagnosis discrete 2
1 Schizophrenia
2 Control
41 Age continuous 0
42 Birthplace discrete 3
1 Statutory
2 Census
3 Rural
43 Upbringingplace discrete 3
1 Statutory
2 Census
3 Rural
44 Livingplace discrete 3
1 Statutory
2 Census
3 Rural
Continuous Factors: Mean: StdDev:
------------------- ----- -------
Left-Lateral-Ventricle 6784.459 3582.583
Left-Inf-Lat-Vent 363.189 163.344
Left-Cerebellum-White-Matter 13393.085 2875.553
Left-Cerebellum-Cortex 50654.337 7634.479
Left-Thalamus-Proper 7044.259 1254.886
Left-Caudate 3267.819 728.738
Left-Putamen 5221.959 863.333
Left-Pallidum 1961.781 357.087
3rd-Ventricle 1068.711 447.579
4th-Ventricle 1673.963 641.339
Brain-Stem 18975.526 3907.934
Left-Hippocampus 3852.407 684.810
Left-Amygdala 1625.463 378.770
CSF 983.626 305.507
Left-Accumbens-area 587.848 155.803
Left-VentralDC 3977.841 673.114
Left-vessel 28.378 21.035
Left-choroid-plexus 558.441 330.333
Right-Lateral-Ventricle 6224.989 3745.143
Right-Inf-Lat-Vent 440.070 168.625
Right-Cerebellum-White-Matter 13111.263 2744.138
Right-Cerebellum-Cortex 52495.385 7167.728
Right-Thalamus-Proper 6732.170 1748.668
Right-Caudate 3305.363 949.074
Right-Putamen 4908.819 1155.840
Right-Pallidum 1774.204 489.167
Right-Hippocampus 3766.470 1019.353
Right-Amygdala 1686.874 437.019
Right-Accumbens-area 539.763 151.780
Right-VentralDC 3818.130 666.970
Right-vessel 23.344 16.649
Right-choroid-plexus 620.948 414.269
WM-hypointensities 4434.148 10311.009
Optic-Chiasm 198.937 65.369
CC_Posterior 973.467 157.378
CC_Mid_Posterior 637.400 597.617
CC_Central 625.374 497.642
CC_Mid_Anterior 681.052 419.940
CC_Anterior 870.274 237.412
Age 31.963 7.019
Number of subjects: 27
Number of factors: 44 (4 discrete, 40 continuous)
Number of classes: 54
Number of regressors: 2214
============================================================
Data table loading completed successfully.
SUBJECTS_DIR is '/usr/local/freesurfer/subjects'
lh-Avg-Intercept-thickness -----------------------
Does the average thickness differ from zero?
Nuisance factors: Age
1.000 1.000 0.000 0.000 0.000 0.000;
lh-Avg-thickness-Right-Amygdala-Cor -----------------------
Does the correlation between thickness and Right-Amygdala, accounting for diagnosis, differ from zero?
Nuisance factors: Age
0.000 0.000 1.000 1.000 0.000 0.000;
lh-Diff-Schizophrenia-Control-Intercept-thickness -----------------------
Does the average thickness differ between Schizophrenia and Control?
Nuisance factors: Age
1.000 -1.000 0.000 0.000 0.000 0.000;
lh-Diff-Schizophrenia-Control-Cor-thickness-Right-Amygdala -----------------------
Does the thickness--Right-Amygdala correlation differ between Schizophrenia and Control?
Nuisance factors: Age
0.000 0.000 1.000 -1.000 0.000 0.000;
I highlighted the discrete factors in yellow color. I wanted to know how to go about this classes such as birthplace, living and upbringing place.
Also, let us know whether the below-pasted information is in the right format for qdec.fsgd file??
Here we have birth, living and upbringing places as main classes and statutory, census and rural as subclasses. So, my question is that the below-pasted classes are ok or not??
If not, just needed your assistance to create fsgd file along with contrasts files.
Finally, can I use the qdec gui for this analysis or just the command-line?
GroupDescriptorFile 1
Title Untitled
MeasurementName thickness
Class BirthplaceStatutory
Class BirthplaceCensus
Class BirthplaceRural
Class UpbringingplaceStatutory
Class UpbringingplaceCensus
Class UpbringingplaceRural
Class LivingplaceStatutory
Class LivingplaceCensus
Class LivingplaceRural
# Class schizophrenia
# Class control
Input 1 BirthplaceStatutory UpbringingplaceStatutory LivingplaceStatutory
Input 3 BirthplaceCensus UpbringingplaceCensus LivingplaceCensus
Input 4 BirthplaceRural UpbringingplaceRural LivingplaceRural
Input 5 BirthplaceStatutory UpbringingplaceStatutory LivingplaceStatutory
Input 6 BirthplaceRural UpbringingplaceCensus LivingplaceCensus
Input 7 BirthplaceCensus UpbringingplaceCensus LivingplaceCensus
Input 8 BirthplaceRural UpbringingplaceRural LivingplaceRural
Input 9 BirthplaceRural UpbringingplaceRural LivingplaceCensus
Input 10 BirthplaceStatutory UpbringingplaceStatutory LivingplaceStatutory
Input 11 BirthplaceStatutory UpbringingplaceStatutory LivingplaceCensus
Input 13 BirthplaceCensus UpbringingplaceCensus LivingplaceCensus
Input 14 BirthplaceCensus UpbringingplaceCensus LivingplaceCensus
Input 15 BirthplaceCensus UpbringingplaceCensus LivingplaceCensus
Input 18 BirthplaceRural UpbringingplaceCensus LivingplaceCensus