Cédric, Does the first column of your Base_File_FreeSurfer.dat contain the freesurfer subject id? the first column must contain that. from the email below, where you show one line of the file, it looks like Subj# is the first column and SubjID is the second.
Nick On Thu, 2013-09-19 at 14:07 +0000, Koolschijn, Cédric wrote: > Dear FS, > > > I' ve run into some strange things in QDEC which I haven't encountered > before. I'm running FS 5.3. > > > First, loading data file in QDEC works, yet terminal output displays > the message below: > > > Data table /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat > loaded. > Verifying subject data.sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '123' in > SUBJECTS_DIR > etc. > > > Until: > Too many subjects not found! > Input table: /home/FreesurferSubjects/qdec/Base_File_FreeSurfer.dat > Subj#, SubjID, Data... > 1 123 423.000000 2.000000 3.000000 23.534247 Male 1.000000 > 2.000000 1461390.000000 490566.000000 755239.000000 706151.000000 > -0.096959 0.641372 -0.09 etc. > > > So it does load the data. Subjectsdir = correct, all files are in > place, no missings or whatsoever. > If I check the dataview option, all looks wel. Also, qdec.fsgd looks > good, no missing values or subjects. > > > This is similar to an old post: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html > > > > > Should I just ignore this? Or is something going wrong? If so, how > should I fix this? > > > > > Second, and this is by far the strangest thing, I have in my > qdec.table.dat file 2 independent groups for a exploration – > validation study. > So, I load my .dat file, including the errors above, then import stats > data => aseg volume =>ICV, and then for a sanity check, in a simple > design I have sex as discrete variable, clinical score as continuous > covariate, and age and ICV as nuisance variables. > This all works perfect. If I select only group 1 (by excluding group > 2), also no problem. Yet, when I only select group 2, with the same > design as stated above, QDEC crashes during loading of the regression > coefficients: > > > (..) > (No errors before) > (..) > Continuous Variable Means (all subjects) > 0 clinvar1 57.0299 8.72632 > 1 AgeYears 22.825 1.72886 > 2 IntraCranialVol 1.10829e+06 129670 > Class Means of each Continuous Variable > 1 sexMale 57.8301 22.7324 1189880.5686 > 2 sexFemale 56.2027 22.9207 1023944.1351 > MatrixMultiply: m1 is null! > > > No such file or directory > For full output, see below > > > > > If I exclude ICV from the analyses, again the analyses work out fine > for group2. Just out of curiosity I tested the same design adding > total gray volume next to ICV, and this works fine. In addition, sex > as discrete variable, clinical score as continuous covariate, and age > and TGV as nuisance variables works also fine. > Separating group2 in a single .dat file didn't resolve this issue. > Somehow ICV is causing this problem, but I can't get my head around > why it does work for group1 or the whole group, but not for group2. > > > In previous posts it was suggested to demean ICV as a solution for > this issue, though this doesn't explain why it works for the other > group? > E.g.: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21744.html > (though in contrast to that post, I don't have missing values (NaN). > > > The only difference between group 1 and 2 is sample size, 204 and 301 > respectively (and of course different subjects, scores, ages etc). > > > Any thoughts on both problems? > > > Many thanks, > Cédric > > > > > Full output after QDEC crash with ICV as nuisance variable for group > 2: > > > lh-Avg-Intercept-thickness ----------------------- > > Does the average thickness differ from zero? > > Nuisance factors: AgeYears IntraCranialVol > > 1.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000; > > > > lh-Avg-thickness-clinvar1-Cor ----------------------- > > Does the correlation between thickness and clinvar1, accounting for > sex, differ from zero? > > Nuisance factors: AgeYears IntraCranialVol > > 0.000 0.000 1.000 1.000 0.000 0.000 0.000 0.000; > > > > lh-Diff-Male-Female-Intercept-thickness ----------------------- > > Does the average thickness differ between Male and Female? > > Nuisance factors: AgeYears IntraCranialVol > > 1.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000; > > > > lh-Diff-Male-Female-Cor-thickness-clinvar1 ----------------------- > > Does the thickness--clinvar1 correlation differ between Male and > Female? > > Nuisance factors: AgeYears IntraCranialVol > > 0.000 0.000 1.000 -1.000 0.000 0.000 0.000 0.000; > > > > ninputs = 301 > > Checking inputs > > nframestot = 301 > > Allocing output > > Done allocing > > nframes = 301 > > Writing to /home/FreesurferSubjects/qdec/Untitled/y.mgh > > gdfReadHeader: > reading /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 clinvar1 57.0299 8.72632 > > 1 AgeYears 22.825 1.72886 > > 2 IntraCranialVol 1.10829e+06 129670 > > Class Means of each Continuous Variable > > 1 sexMale 57.8301 22.7324 1189880.6867 > > 2 sexFemale 56.2027 22.9207 1023944.2196 > > INFO: gd2mtx_method is dods > > Reading source > surface /home/FreesurferSubjects/fsaverage/surf/lh.white > > Number of vertices 163842 > > Number of faces 327680 > > Total area 65416.648438 > > AvgVtxArea 0.399267 > > AvgVtxDist 0.721953 > > StdVtxDist 0.195470 > > > > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/FreesurferSubjects/qdec > > cmdline mri_glmfit --y /home/FreesurferSubjects/qdec/Untitled/y.mgh > --fsgd /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd dods > --glmdir /home/FreesurferSubjects/qdec/Untitled --surf fsaverage lh > --label /home/FreesurferSubjects/fsaverage/label/lh.aparc.label > --C > /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > --C > /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar1-Cor.mat > --C > /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat > --C > /home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-clinvar1.mat > > > sysname Linux > > hostname tux08 > > machine x86_64 > > user cedric > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y /home/FreesurferSubjects/qdec/Untitled/y.mgh > > logyflag 0 > > usedti 0 > > FSGD /home/FreesurferSubjects/qdec/Untitled/qdec.fsgd > > labelmask /home/FreesurferSubjects/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /home/FreesurferSubjects/qdec/Untitled > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /home/FreesurferSubjects/qdec/Untitled > > Loading y from /home/FreesurferSubjects/qdec/Untitled/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /home/FreesurferSubjects/qdec/Untitled/Xg.dat > > Normalized matrix condition is 2142.57 > > Matrix condition is 1e+08 > > Found 148151 points in label. > > Pruning voxels by thr: 0.000000 > > Found 148025 voxels in mask > > Saving mask to /home/FreesurferSubjects/qdec/Untitled/mask.mgh > > Reshaping mriglm->mask... > > search space = 73649.347769 > > DOF = 293 > > Starting fit and test > > Fit completed in 0.24555 minutes > > Computing spatial AR1 on surface > > Residual: ar1mn=0.995767, ar1std=0.000990, gstd=6.213820, > fwhm=14.632428 > > Writing results > > lh-Avg-Intercept-thickness > > maxvox sig=1e+10 F=293.283 at index 274 0 0 seed=1379991059 > > lh-Avg-thickness-clinvar1-Cor > > maxvox sig=3.50473 F=13.3076 at index 30493 0 0 seed=1379991059 > > lh-Diff-Male-Female-Intercept-thickness > > maxvox sig=3.35828 F=12.6481 at index 14613 0 0 seed=1379991059 > > lh-Diff-Male-Female-Cor-thickness-clinvar1 > > maxvox sig=-2.55573 F=9.09923 at index 128858 0 > 0 seed=1379991059 > > mri_glmfit done > > ninputs = 4 > > Checking inputs > > nframestot = 4 > > Allocing output > > Done allocing > > nframes = 4 > > Writing to /home/FreesurferSubjects/qdec/Untitled/contrasts.sig.mgh > > reading colortable from annotation file... > > colortable with 36 entries read > (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > > reading colortable from annotation file... > > colortable with 36 entries read > (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > > gdfReadHeader: reading /home/FreesurferSubjects/qdec/Untitled/y.fsgd > > INFO: ignoring tag Creator > > INFO: ignoring tag SUBJECTS_DIR > > INFO: ignoring tag SynthSeed > > INFO: NOT demeaning continuous variables > > Continuous Variable Means (all subjects) > > 0 clinvar1 57.0299 8.72632 > > 1 AgeYears 22.825 1.72886 > > 2 IntraCranialVol 1.10829e+06 129670 > > Class Means of each Continuous Variable > > 1 sexMale 57.8301 22.7324 1189880.5686 > > 2 sexFemale 56.2027 22.9207 1023944.1351 > > MatrixMultiply: m1 is null! > > > > No such file or directory > > > > > > > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. 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