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
