Cédric, can you send me the .dat file?
N. On Wed, 2013-09-25 at 16:58 +0000, Koolschijn, Cédric wrote: > Hi Nick, > > The first column is fsid, the reason why you see a number before fsid, is > because it's a line-number copied from g/n-edit. > > Cheers > Cédric > > > > > -----Original Message----- > From: Nick Schmansky <ni...@nmr.mgh.harvard.edu> > Date: Wednesday, September 25, 2013 6:44 PM > To: Cédric Koolschijn <p.c.m.p.koolsch...@uva.nl> > Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] QDEC double trouble: 1. VerifySubjects 2. > MatrixMultiply: m1 is null! > > >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-thickne > >>ss.mat --C > >>/home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Avg-thickness-clinvar > >>1-Cor.mat --C > >>/home/FreesurferSubjects/qdec/Untitled/contrasts/lh-Diff-Male-Female-Inte > >>rcept-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_desik > >>an_killiany.txt) > >> > >> reading colortable from annotation file... > >> > >> colortable with 36 entries read > >> (originally > >>/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desik > >>an_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 > > > > > > > > > >The information in this e-mail is intended only for the person to whom it > >is > >addressed. If you believe this e-mail was sent to you in error and the > >e-mail > >contains patient information, please contact the Partners Compliance > >HelpLine at > >http://www.partners.org/complianceline . If the e-mail was sent to you in > >error > >but does not contain patient information, please contact the sender and > >properly > >dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
