The demeaning/mean centering worked a treat! Thank you freesurfer experts! Laura.
On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > If it's working with demeaning, then that was the problem. The subjects > with NaNs are going to be excluded entirely as we have no way to estimate > missing fields. > doug > > Laura Tully wrote: > >> Hi Nick and Doug, >> Thanks for the help, I'll give the demeaning a try. >> Re: the missing values - all my missing data points are denoted with NaN >> so that I can include those subjects on the measures that they do have, but >> exclude them on measures they don't have (I think this is the only way to >> load the data table if there are missing values, is that correct?) This >> seems to be working fine when I do not include ICV as a nuisance variable. >> Do you think that these non-number cells are causing the issue? (I have >> check the data table to make sure that there are no empty cells). >> Laura. >> On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> In the terminal output, it says that it will exclude a subject >> because there is a NaN data point. NaN = "not a number". Check >> your data table to make sure that everything is ok. >> doug >> >> >> Nick Schmansky wrote: >> >> it means to subtract the mean of the icv values from each. >> that way the >> values are close to zero, and closer in value to the other >> values in the >> glm (which seems to make the glm happier). >> >> n. >> >> On Thu, 2012-03-01 at 11:04 -0500, Laura Tully wrote: >> >> Hi Doug, >> >> I saw on a previous mailing earlier this week that someone >> has been >> having a similar error and that your advice was to demean >> the ICV. I >> apologise if this is a stupid question, but what does it >> mean to >> "demean"? And, how do i do that? >> >> Thanks in advance! >> >> Laura. >> On Wed, Feb 29, 2012 at 2:27 PM, Laura Tully >> <tully.la...@googlemail.com >> <mailto:tully.laura@**googlemail.com<tully.la...@googlemail.com>>> >> wrote: >> Hi Doug, Below is the output in the >> terminal window from running the >> analysis to the crash. Attached are the qdec.fsgd >> and y.fsgd >> files from the qdec output. I'm not actually sure >> what these >> file represent - could you enlighten me? >> Thanks! >> Laura. Number of subjects: 55 >> Number of factors: 48 (2 discrete, 46 continuous) >> Number of classes: 4 >> Number of regressors: 188 >> ==============================** >> ============================== >> WARNING: will exclude subject 27115 from >> analysis due to NaN >> data point! >> WARNING: will exclude subject 27211 from >> analysis due to NaN >> data point! >> WARNING: will exclude subject 27212 from >> analysis due to NaN >> data point! >> lh-Avg-Intercept-thickness ----------------------- >> Does the average thickness differ from zero? >> Nuisance factors: IntraCranialVol >> 1.000 1.000 0.000 0.000 0.000 0.000; >> lh-Avg-thickness-CPT_IP-Cor >> ----------------------- >> Does the correlation between thickness and CPT_IP, >> accounting >> for group, differ from zero? >> Nuisance factors: IntraCranialVol >> 0.000 0.000 1.000 1.000 0.000 0.000; >> lh-Diff-HC-SZ-Intercept-**thickness >> ----------------------- >> Does the average thickness differ between HC and SZ? >> Nuisance factors: IntraCranialVol >> 1.000 -1.000 0.000 0.000 0.000 0.000; >> lh-Diff-HC-SZ-Cor-thickness-**CPT_IP >> ----------------------- >> Does the thickness--CPT_IP correlation differ >> between HC and >> SZ? >> Nuisance factors: IntraCranialVol >> 0.000 0.000 1.000 -1.000 0.000 0.000; >> ninputs = 52 >> Checking inputs >> nframestot = 52 >> Allocing output >> Done allocing >> nframes = 52 >> Writing >> to >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/y.mgh >> gdfReadHeader: >> reading >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/qdec.fsgd >> INFO: DeMeanFlag keyword not found, DeMeaning will >> NOT be >> done. >> Continuous Variable Means (all subjects) >> 0 CPT_IP 2.83135 0.695203 >> 1 IntraCranialVol 1.29955e+06 249396 >> Class Means of each Continuous Variable >> 1 groupHC 3.0515 1340186.4398 2 groupSZ >> 2.5936 1255661.8075 INFO: gd2mtx_method is dods >> Reading source >> surface >> /ncf/snp/04/SCORE/freesurfer_**analysis/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 1.196.2.6 2011/05/05 >> 20:54:25 greve Exp $ >> cwd /ncf/snp/04/SCORE/freesurfer_**analysis/qdec >> cmdline mri_glmfit >> --y >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/y.mgh >> --fsgd >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/qdec.fsgd >> dods --glmdir >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV >> --surf fsaverage lh --label >> /ncf/snp/04/SCORE/freesurfer_**analysis/fsaverage/label/lh.** >> aparc.label >> --C >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/contrasts/lh-Avg-**Intercept-thickness.mat >> --C >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/contrasts/lh-Avg-**thickness-CPT_IP-Cor.mat >> --C >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/contrasts/lh-**Diff-HC-SZ-Intercept-**thickness.mat >> --C >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/contrasts/lh-**Diff-HC-SZ-Cor-thickness-CPT_**IP.mat >> sysname Linux >> hostname ncfws17.rc.fas.harvard.edu >> >> <http://ncfws17.rc.fas.**harvard.edu<http://ncfws17.rc.fas.harvard.edu> >> > >> >> machine x86_64 >> user ltully >> FixVertexAreaFlag = 1 >> UseMaskWithSmoothing 1 >> OneSampleGroupMean 0 >> y /ncf/snp/04/SCORE/freesurfer_** >> analysis/qdec/lh_thick_10mm_**groupCPT_ICV/y.mgh >> logyflag 0 >> usedti 0 >> FSGD >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/qdec.fsgd >> labelmask >> /ncf/snp/04/SCORE/freesurfer_**analysis/fsaverage/label/lh.** >> aparc.label >> maskinv 0 >> glmdir >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV >> IllCondOK 0 >> ReScaleX 1 >> DoFFx 0 >> Creating output >> directory >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV >> Loading y >> from >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/y.mgh >> INFO: gd2mtx_method is dods >> Saving design matrix >> to >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/Xg.dat >> Normalized matrix condition is 263.453 >> Matrix condition is 1e+08 >> Found 148151 points in label. >> Pruning voxels by thr: 0.000000 >> Found 148025 voxels in mask >> Saving mask >> to >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/mask.mgh >> Reshaping mriglm->mask... >> search space = 73649.347769 >> DOF = 46 >> Starting fit and test >> Fit completed in 0.11535 minutes >> Computing spatial AR1 on surface >> Residual: ar1mn=0.996105, ar1std=0.001362, >> gstd=6.478212, >> fwhm=15.255024 >> Writing results >> lh-Avg-Intercept-thickness >> maxvox sig=21.5032 F=315.736 at index 99361 0 0 >> seed=1330929601 >> lh-Avg-thickness-CPT_IP-Cor >> maxvox sig=3.23567 F=13.661 at index 155907 0 0 >> seed=1330929601 >> lh-Diff-HC-SZ-Intercept-**thickness >> maxvox sig=-2.63051 F=10.3802 at index 6941 0 0 >> seed=1330929601 >> lh-Diff-HC-SZ-Cor-thickness-**CPT_IP >> maxvox sig=-3.05362 F=12.6489 at index >> 145301 0 0 >> seed=1330929601 >> mri_glmfit done >> ninputs = 4 >> Checking inputs >> nframestot = 4 >> Allocing output >> Done allocing >> nframes = 4 >> Writing >> to >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/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 >> /ncf/snp/04/SCORE/freesurfer_**analysis/qdec/lh_thick_10mm_** >> groupCPT_ICV/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 CPT_IP 2.83135 0.695203 >> 1 IntraCranialVol 1.29955e+06 249396 >> Class Means of each Continuous Variable >> 1 groupHC 3.0515 1340187.1111 2 groupSZ >> 2.5936 1255662.3200 MatrixMultiply: m1 is null! >> No such file or directory >> On Tue, Feb 28, 2012 at >> 5:51 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> Can you send the fsgd file that is created? >> Also, >> please send more text output. It's hard to >> tell from a >> single line. >> doug >> Laura Tully wrote: >> Hi, I am >> trying to run a between group analysis in >> QDEC whilst controlling for >> intrancranial >> volume. The design has one dichotomous >> variable (group2, group2), one >> continuous >> (performance on behavioral task), >> and one >> nuisance variable (intracranial >> volume). each >> time I run it qec crashes with the >> following >> error: >> MatrixMultiply: ml null! >> What does this error mean and how >> can I fix >> it? What is >> odd is that this error does not seem >> to be consistently reproducible - after >> successfully running the analyses >> without >> controlling for ICV, I was then >> able to run it >> with ICV as a nuisance factor. >> Thank you! >> Laura. -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 806 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> >> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu**> >> <mailto:ltu...@fas.harvard.edu >> >> <mailto:ltu...@fas.harvard.edu**>> >> >> ------------------------------** >> ------------------------------**------------ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> -- Douglas >> N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 >> <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> >> Bugs: >> >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/** >> facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> >> 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<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. >> -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 806 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu** >> > >> +1 857 207 5509 <tel:%2B1%20857%20207%205509> >> >> >> >> >> -- Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 840 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu**> >> >> >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 >> <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> >> >> >> >> -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 840 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu**> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu
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