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.
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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 greve@nmr.mgh.harvard.eduwrote:
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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu**
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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.
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.laura@googlemail.comwrote:
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 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 < greve@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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu**
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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 ltully@fas.harvard.edu +1 857 207 5509
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.laura@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 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 <greve@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 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. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu +1 857 207 5509-- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.laura@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 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 <greve@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 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. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu +1 857 207 5509-- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 greve@nmr.mgh.harvard.eduwrote:
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.laura@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 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 greve@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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu**
------------------------------**------------------------------**
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.** edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/** fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/**compliancelinehttp://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 ltully@fas.harvard.edu +1 857 207 5509
-- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 <greve@nmr.mgh.harvard.edu mailto:greve@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.laura@googlemail.com <mailto:tully.laura@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> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> <mailto:ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>> ------------------------------------------------------------------------ _______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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> FileDrop: 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 . 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 ltully@fas.harvard.edu <mailto:ltully@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> _______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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> 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 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu
The demeaning/mean centering worked a treat! Thank you freesurfer experts!
Laura.
On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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 < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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.laura@googlemail.com <mailto:tully.laura@**googlemail.com<tully.laura@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.eduhttp://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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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
ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu** <mailto:ltully@fas.harvard.edu
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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 ltully@fas.harvard.edu <mailto:ltully@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu**> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@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
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-- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu mailto:ltully@fas.harvard.edu**
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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btw, to tie-in and follow-up on a related posted question about missing values, if NaN is used for the missing value (as you did), then qdec will automatically exclude that subject in an analysis if that variable is used. the rejected subject(s) will be printed to the terminal.
N.
On Thu, 2012-03-01 at 13:29 -0500, Laura Tully wrote:
The demeaning/mean centering worked a treat! Thank you freesurfer experts!
Laura.
On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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.laura@googlemail.com <mailto:tully.laura@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> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> <mailto:ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>> ------------------------------------------------------------------------ _______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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> FileDrop: 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 . 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 ltully@fas.harvard.edu <mailto:ltully@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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> _______________________________________________ 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 greve@nmr.mgh.harvard.edu <mailto:greve@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> 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 ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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-- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
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Nick Schmansky