[Freesurfer] Qdec Error: MatrixMultiply: ml is null!
Hi, I am trying to run a between group analysis in QDEC whilst controlling for intrancranial volume. The design has one dichotomous variable (group2, group2), one continuous (performance on behavioral task), and one nuisance variable (intracranial volume). each time I run it qec crashes with the following error: MatrixMultiply: ml null! What does this error mean and how can I fix it? What is odd is that this error does not seem to be consistently reproducible - after successfully running the analyses without controlling for ICV, I was then able to run it with ICV as a nuisance factor. Thank you! Laura. -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!
5301 0 0seed=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. 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 wrote: > Can you send the fsgd file that is created? Also, please send more text > output. It's hard to tell from a single line. > doug > > Laura Tully wrote: > >> Hi, >> I am trying to run a between group analysis in QDEC whilst controlling >> for intrancranial volume. The design has one dichotomous variable (group2, >> group2), one continuous (performance on behavioral task), and one nuisance >> variable (intracranial volume). each time I run it qec crashes with the >> following error: >>MatrixMultiply: ml null! >> >> What does this error mean and how can I fix it? >> What is odd is that this error does not seem to be consistently >> reproducible - after successfully running the analyses without controlling >> for ICV, I was then able to run it with ICV as a nuisance factor. >> Thank you! >> Laura. >> -- >> Laura Tully >> Social Neuroscience & Psychopathology >> Harvard University >> 806 William James Hall >> 33 Kirkland St >> Cambridge, MA 02138 >> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu**> >> >> >> --**--** >> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Laura Tully Social Neuroscience & Psychopathology Harvard University 806 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu +1 857 207 5509 y.fsgd Description: Binary data qdec.fsgd Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!
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 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 faces327680 > 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
Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!
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 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 >>> 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
Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!
The demeaning/mean centering worked a treat! Thank you freesurfer experts! Laura. On Thu, Mar 1, 2012 at 11:36 AM, Douglas N Greve wrote: > If it's working with demeaning, then that was the problem. The subjects > with NaNs are going to be excluded entirely as we have no way to estimate > missing fields. > doug > > Laura Tully wrote: > >> Hi Nick and Doug, >> Thanks for the help, I'll give the demeaning a try. >> Re: the missing values - all my missing data points are denoted with NaN >> so that I can include those subjects on the measures that they do have, but >> exclude them on measures they don't have (I think this is the only way to >> load the data table if there are missing values, is that correct?) This >> seems to be working fine when I do not include ICV as a nuisance variable. >> Do you think that these non-number cells are causing the issue? (I have >> check the data table to make sure that there are no empty cells). >> Laura. >> On Thu, Mar 1, 2012 at 11:14 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> 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 >>><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 >>
[Freesurfer] Qdec Error in analyze: command failed
Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table loading completed successfully. SUBJECTS_DIR is '/ncf/snp/04/SCORE/freesurfer_analysis' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? Nuisance factors: ICV_Mean_Centered 1.000 0.000 0.000; lh-Avg-thickness-Social_Fx-Cor --- Does the correlation between thickness and Social_Fx differ from zero? Nuisance factors: ICV_Mean_Centered 0.000 1.000 0.000; sh: ICV/y.mgh: No such file or directory ninputs = 29 Checking inputs nframestot = 29 Allocing output Done allocing nframes = 29 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx unknown file type for file (/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx) Error in Analyze: command failed: mri_concat /ncf/snp/04/SCORE/freesurfer_analysis/27119/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27120/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27121/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27122/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27125/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27127/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27131/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27140/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27145/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27160/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27164/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27191/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27193/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27194/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27195/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27196/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27199/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27201/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27203/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27204/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27205/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27206/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27208/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27210/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27211/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27212/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27213/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27216/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27218/surf/lh.thickness.fwhm10.fsaverage.mgh --o /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx&ICV/y.mgh -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: Qdec Error in analyze: command failed
Hi All, Just wanted to follow up on my message below. Thank you! Laura. -- Forwarded message -- From: Laura Tully Date: Mon, Mar 5, 2012 at 2:03 PM Subject: Qdec Error in analyze: command failed To: freesurfer@nmr.mgh.harvard.edu Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table loading completed successfully. SUBJECTS_DIR is '/ncf/snp/04/SCORE/freesurfer_analysis' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? Nuisance factors: ICV_Mean_Centered 1.000 0.000 0.000; lh-Avg-thickness-Social_Fx-Cor --- Does the correlation between thickness and Social_Fx differ from zero? Nuisance factors: ICV_Mean_Centered 0.000 1.000 0.000; sh: ICV/y.mgh: No such file or directory ninputs = 29 Checking inputs nframestot = 29 Allocing output Done allocing nframes = 29 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx unknown file type for file (/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx) Error in Analyze: command failed: mri_concat /ncf/snp/04/SCORE/freesurfer_analysis/27119/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27120/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27121/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27122/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27125/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27127/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27131/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27140/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27145/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27160/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27164/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27191/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27193/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27194/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27195/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27196/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27199/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27201/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27203/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27204/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27205/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27206/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27208/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27210/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27211/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27212/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27213/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27216/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27218/surf/lh.thickness.fwhm10.fsaverage.mgh --o /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx&ICV/y.mgh -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
