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 <vittalkor...@gmail.com > <mailto:vittalkor...@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 > > > */ > /* > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
