Sorry, hit the send before I was ready. I was also going to point out that mri_glmfit will zero-out a voxel unless it finds that all inputs are non-zero (pruning). It looks like it could not find any voxels that met this criterion. doug
Douglas N Greve wrote: > Did the data set change between the two analyses? The > > KingLab wrote: > >> Hello Doug- >> In going through the threads for freesurfer, I found the following which >> also describes the issue I am having. However, the error arises for me while >> running a collection of brains through qdec, so I have not been running the >> script directly in order to simply add the --no-prune tag. I am running the >> qdec analysis on new measurements created specifically for analysis in our >> lab. Someone prior to me set up everything for the qdec analysis to work >> fine with another database, and was halfway through another brain database >> when I picked up. For this database, the prior person completed the >> measurement entitled middle30.asc, which works fine. When using the same >> .dat file for the database, and the only difference is using the measure of >> middle45.asc, no data is mapped to the brains. In looking through the code, >> the same error appeared to happen in the mri_glmfit command in the same >> place. -qcache has been run for all of the brains for the new measurement, >> and the middle30.asc files appear similar in structure to the middle45.asc >> files, as would be expected. Why would it be pruning the one measurement >> and not the other? Where can I look to solve the issue to run the data in >> qdec to compare the measurements? If I just run mri_glmfit with --no-prune, >> will qdec read it in without overwriting it automatically? I have a feeling >> I missed something in preparing the new region that the person I took over >> for has done for the other measurements, but I'm not sure what it is or >> where to look for it. Any help would be appreciated. Thanks! >> Below I have included the output for both measurements. The codes appear >> identical up until after the pruning command comes about which provides 0 >> voxels. >> middle30.asc >> >> lh-Avg-Intercept-middle30.asc ----------------------- >> >> Does the average middle30.asc differ from zero? >> >> 1.000 1.000; >> >> lh-Diff-Normal-AD-Intercept-middle30.asc ----------------------- >> >> Does the average middle30.asc differ between Normal and AD? >> >> 1.000 -1.000; >> >> ninputs = 188 >> >> Checking inputs >> >> nframestot = 188 >> >> Allocing output >> >> nframes = 188 >> >> Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >> >> gdfReadHeader: reading >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >> >> INFO: demeaning continous variables >> >> Continuous Variable Means (all subjects) >> >> Class Means of each Continuous Variable >> >> 1 Diagnosis2Normal >> >> 2 Diagnosis2AD >> >> INFO: gd2mtx_method is dods >> >> Reading source surface >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white >> >> reading group avg surface area 822 cm^2 from file >> >> Reading in average area >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >> >> 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 1.138.2.12 2009/06/03 00:06:45 greve Exp $ >> >> cwd /Volumes/MacintoshHD2/ADNI-PreProcessed >> >> cmdline mri_glmfit --y >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods >> --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf >> fsaverage lh --label >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> --C >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle30.asc.mat >> >> --C >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle30.asc.mat >> >> >> >> sysname Darwin >> >> hostname b417w74-106.med.utah.edu >> >> machine i386 >> >> user kinglab >> >> FixVertexAreaFlag = 1 >> >> UseMaskWithSmoothing 1 >> >> OneSampleGroupMean 0 >> >> y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >> >> logyflag 0 >> >> usedti 0 >> >> FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >> >> labelmask >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> >> maskinv 0 >> >> glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >> >> IllCondOK 0 >> >> DoFFx 0 >> >> Creating output directory >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >> >> Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >> >> INFO: gd2mtx_method is dods >> >> Saving design matrix to >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat >> >> Matrix condition is 1 >> >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> >> Found 149955 points in label. >> >> Pruning voxels by thr: 0.000000 >> >> Found 149953 voxels in mask >> >> Saving mask to >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh >> >> search space = 75250.1 >> >> DOF = 186 >> >> Starting fit and test >> >> Fit completed in 0.0740167 minutes >> >> Computing spatial AR1 on surface >> >> INFO: fwhmFromAR1: Fixing group surface area >> >> Residual: ar1mn=0.998860, ar1std=0.000986, gstd=11.981826, fwhm=28.215043 >> >> Writing results >> >> lh-Avg-Intercept-middle30.asc >> >> maxvox sig=1e+10 F=86188.1 at index 0 0 0 seed=1324082303 >> >> lh-Diff-Normal-AD-Intercept-middle30.asc >> >> maxvox sig=9.81891 F=46.013 at index 70329 0 0 seed=1324082303 >> >> mri_glmfit done >> >> ninputs = 2 >> >> Checking inputs >> >> nframestot = 2 >> >> Allocing output >> >> nframes = 2 >> >> Writing to >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh >> >> reading group avg surface area 822 cm^2 from file >> >> Reading in average area >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >> >> reading group avg surface area 1041 cm^2 from file >> >> Reading in average area >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh >> >> reading group avg surface area 822 cm^2 from file >> >> reading colortable from annotation file... >> >> colortable with 36 entries read (originally >> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> >> reading colortable from annotation file... >> >> colortable with 36 entries read (originally >> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> >> gdfReadHeader: reading >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd >> >> INFO: ignoring tag Creator >> >> INFO: ignoring tag SUBJECTS_DIR >> >> INFO: ignoring tag SynthSeed >> >> INFO: demeaning continous variables >> >> Continuous Variable Means (all subjects) >> >> Class Means of each Continuous Variable >> >> 1 Diagnosis2Normal >> >> 2 Diagnosis2AD >> >> >> >> ============================================================ >> >> Completed loading of analyzed data. >> >> >> >> Middle45.asc >> >> lh-Avg-Intercept-middle45.asc ----------------------- >> >> Does the average middle45.asc differ from zero? >> >> 1.000 1.000; >> >> lh-Diff-Normal-AD-Intercept-middle45.asc ----------------------- >> >> Does the average middle45.asc differ between Normal and AD? >> >> 1.000 -1.000; >> >> ninputs = 188 >> >> Checking inputs >> >> nframestot = 188 >> >> Allocing output >> >> nframes = 188 >> >> Writing to /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >> >> gdfReadHeader: reading >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >> >> INFO: demeaning continous variables >> >> Continuous Variable Means (all subjects) >> >> Class Means of each Continuous Variable >> >> 1 Diagnosis2Normal >> >> 2 Diagnosis2AD >> >> INFO: gd2mtx_method is dods >> >> Reading source surface >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white >> >> reading group avg surface area 822 cm^2 from file >> >> Reading in average area >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >> >> 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 1.138.2.12 2009/06/03 00:06:45 greve Exp $ >> >> cwd /Volumes/MacintoshHD2/ADNI-PreProcessed >> >> cmdline mri_glmfit --y >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh --fsgd >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd dods >> --glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled --surf >> fsaverage lh --label >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> --C >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Avg-Intercept-middle45.asc.mat >> >> --C >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts/lh-Diff-Normal-AD-Intercept-middle45.asc.mat >> >> >> >> sysname Darwin >> >> hostname b417w74-106.med.utah.edu >> >> machine i386 >> >> user kinglab >> >> FixVertexAreaFlag = 1 >> >> UseMaskWithSmoothing 1 >> >> OneSampleGroupMean 0 >> >> y /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >> >> logyflag 0 >> >> usedti 0 >> >> FSGD /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/qdec.fsgd >> >> labelmask >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> >> maskinv 0 >> >> glmdir /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >> >> IllCondOK 0 >> >> DoFFx 0 >> >> Creating output directory >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled >> >> Loading y from /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.mgh >> >> INFO: gd2mtx_method is dods >> >> Saving design matrix to >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/Xg.dat >> >> Matrix condition is 1 >> >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/label/lh.cortex.label >> >> Found 149955 points in label. >> >> Pruning voxels by thr: 0.000000 >> >> Found 0 voxels in mask >> >> Saving mask to >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/mask.mgh >> >> search space = 0 >> >> DOF = 186 >> >> Starting fit and test >> >> Fit completed in 0.0002 minutes >> >> Computing spatial AR1 on surface >> >> INFO: fwhmFromAR1: Fixing group surface area >> >> WARNING: ar1 = nan <= 0. Setting fwhm to 0. >> >> Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000 >> >> Writing results >> >> lh-Avg-Intercept-middle45.asc >> >> maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 >> >> lh-Diff-Normal-AD-Intercept-middle45.asc >> >> maxvox sig=0 F=0 at index 0 0 0 seed=1323815913 >> >> mri_glmfit done >> >> ninputs = 2 >> >> Checking inputs >> >> nframestot = 2 >> >> Allocing output >> >> nframes = 2 >> >> Writing to >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/contrasts.sig.mgh >> >> reading group avg surface area 822 cm^2 from file >> >> Reading in average area >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.white.avg.area.mgh >> >> reading group avg surface area 1041 cm^2 from file >> >> Reading in average area >> /Volumes/MacintoshHD2/ADNI-PreProcessed/fsaverage/surf/lh.pial.avg.area.mgh >> >> reading group avg surface area 822 cm^2 from file >> >> reading colortable from annotation file... >> >> colortable with 36 entries read (originally >> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> >> reading colortable from annotation file... >> >> colortable with 36 entries read (originally >> /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.txt) >> >> gdfReadHeader: reading >> /Volumes/MacintoshHD2/ADNI-PreProcessed/qdec/Untitled/y.fsgd >> >> INFO: ignoring tag Creator >> >> INFO: ignoring tag SUBJECTS_DIR >> >> INFO: ignoring tag SynthSeed >> >> INFO: demeaning continous variables >> >> Continuous Variable Means (all subjects) >> >> Class Means of each Continuous Variable >> >> 1 Diagnosis2Normal >> >> 2 Diagnosis2AD >> >> >> >> ============================================================ >> >> Completed loading of analyzed data. >> >> Thank you! >> >> Kyle Hansen >> >> Research Assistant - AIAL >> >> University of Utah >> >> Hi Kevin, the problem is that once you threshold for >0, there are no >> voxels that have non-zero values in all of the input subjects. Such >> voxels are "pruned" because there is not a good model for them. The GLM >> code does not do a different design at each voxels. In general, doing >> such thresholding is bad statistically. If you really want to do it, run >> it with --no-prune. >> >> doug >> >> kevin bickart wrote: >> >>> Hi all, >>> >>> I am conducting a contrast of z (r) maps from 3 seed-based >>> resting-state networks (e.g., 1 > 2 and 3). To eliminate the influence >>> of anticorrelations on the contrast results, I thresholded the z (r) >>> maps at 0 before running mri_glmfit, thereby eliminating voxels with >>> negative z (r) values. The command completed successfully but the >>> resulting sig maps did not contain voxels with any values. I have >>> attached the fsgd and contrast files and pasted the command and output >>> below. Can anyone identify the problem here? >>> Thanks, >>> Kevin >>> >>> *Potentially problematic portion of output:* >>> Pruning voxels by thr: 0.000000 >>> Found 0 voxels in mask >>> Saving mask to LR_Amy_lOFC2_glm2/mask.mgh >>> search space = 0.000000 >>> >>> *Entire command and output: * >>> [kreature:kbickart_fcmap_ASN_Anchor_AmyPks_buckner_YC] >>> (nmr-stable5.1-env) mri_glmfit --y LR_Amy_lOFCpk2 >>> _vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep --fsgd >>> /autofs/homes/006/kbickart/AmySubNet_glm/pa >>> ired3.fsgd doss --C >>> /autofs/homes/006/kbickart/AmySubNet_glm/paired.mat --glmdir >>> LR_Amy_lOFC2_glm2 >>> gdfReadHeader: reading >>> /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. >>> Continuous Variable Means (all subjects) >>> 0 roi1_vs_roi2_vs_roi3 0 0.707107 >>> Class Means of each Continuous Variable >>> 1 Class_081028_BC77WB 0.0000 >>> 2 Class_081028_XE45TK 0.0000 >>> 3 Class_081028_YY28TK 0.0000 >>> .... >>> $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ >>> cwd >>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckne >>> r_YC >>> cmdline mri_glmfit --y >>> LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz --allowsubjrep >>> --fsgd /autof >>> s/homes/006/kbickart/AmySubNet_glm/paired3.fsgd doss --C >>> /autofs/homes/006/kbickart/AmySubNet_glm/paired >>> .mat --glmdir LR_Amy_lOFC2_glm2 >>> sysname Linux >>> hostname kreature >>> machine x86_64 >>> user kbickart >>> FixVertexAreaFlag = 1 >>> UseMaskWithSmoothing 1 >>> OneSampleGroupMean 0 >>> y >>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_AmyPks_buckn >>> er_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz >>> logyflag 0 >>> usedti 0 >>> FSGD /autofs/homes/006/kbickart/AmySubNet_glm/paired3.fsgd >>> glmdir LR_Amy_lOFC2_glm2 >>> IllCondOK 0 >>> ReScaleX 1 >>> DoFFx 0 >>> Creating output directory LR_Amy_lOFC2_glm2 >>> Loading y from >>> /autofs/cluster/animal/rs-fmri/YC/GROUP_STATS/kbickart/FCMAP/kbickart_fcmap_ASN_Anchor_Am >>> yPks_buckner_YC/LR_Amy_lOFCpk2_vs_vmPFCpk2_and_cACCpk2_pos_4D.nii.gz >>> llINFO: gd2mtx_method is doss >>> Saving design matrix to LR_Amy_lOFC2_glm2/Xg.dat >>> Normalized matrix condition is 1 >>> Matrix condition is 44.5 >>> Pruning voxels by thr: 0.000000 >>> Found 0 voxels in mask >>> Saving mask to LR_Amy_lOFC2_glm2/mask.mgh >>> search space = 0.000000 >>> DOF = 177 >>> Starting fit and test >>> Fit completed in 0.0148667 minutes >>> Computing spatial AR1 in volume. >>> fMRIspatialAR1(): hit 0 voxels >>> WARNING: no voxels in AR1 computation >>> Residual: ar1mn = (nan,nan,nan) fwhm = (nan,nan,nan) nan >>> Writing results >>> paired >>> maxvox sig=0 F=0 at index 0 0 0 seed=1321328111 >>> mri_glmfit done >>> >>> >>> >>> -- >>> Kevin Bickart >>> MD-PhD Student >>> Department of Anatomy and Neurobiology >>> Boston University School of Medicine >>> >>> >>> live UP to it >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> -- >> 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 >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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. >> > > -- 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 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
