That looks like the terminal output for qdec. You cannot use qdec with your design. If you have questions about the FSGD, I'll be happy to answer them.

On 10/16/2018 11:00 AM, vittal korann wrote:

External Email - Use Caution

Hi Doug,

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/* */ /* */Thank you/* */ /* */Best/* */Vittal/*

*/ /*

On Mon, Oct 15, 2018 at 7:45 PM vittal korann <vittalkorann@gmail.com mailto:vittalkorann@gmail.com> wrote:

Hi Doug,

Recently I started working on freesurfer for volume based
analysis. For QDEC, I need to include more than 2 variables. For
example if I include patients who hail from different places like
statutory town, census town and rural. In present scenario, can I
include all three as covariates.
Here is the error that qdec showing while running GLM:

"ERROR: Subject 2 seems to have a mismatched number of discrete
factors (expected 4, found 1)"
"Reading source surface
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified."
"Error in Analyze: command fai;ed mri_glmfit --y
/usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd
/usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir
/usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh
-label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label"

Could you help us out in this regard.

Would appreciate any help!!

Korann


*/
/*

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