Re: [Freesurfer] Help with QDEC error
Hello again, I also tried the command line options. I get an error for ill-conditioned matrix. Could it be because of possible correlations between covariates? For example I am using Age and mean thickness, should I just use one of them? Here is the error: wrls-guest-166-198:subjects manishdalwani$ mri_glmfit --y lh.thickness.CD.10.mlh.thickness.CD.10.mgh lh.thickness.CD.10.mris_preproc.log wrls-guest-166-198:subjects manishdalwani$ mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir gdfReadHeader: reading FSGD_CD.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 16.6492 1.13124 1 Meanthickness 2.4772 0.0616129 2 IQ 98.08 8.24097 3 CD 6.44 2.77244 Class Means of each Continuous Variable 1 PATIENTS 16.6492 2.4772 98.0800 6.4400 INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/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 /Applications/freesurfer/subjects cmdline mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir sysname Darwin hostname wrls-guest-166-198.ucdenver.edu machine i386 user manishdalwani FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.thickness.CD.10.mgh logyflag 0 usedti 0 FSGD FSGD_CD.fsgd labelmask /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.thickness_CD.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.thickness_CD.glmdir Loading y from /Applications/freesurfer/subjects/lh.thickness.CD.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.thickness_CD.glmdir/Xg.dat Normalized matrix condition is 22815.1 Design matrix -- 1.000 15.320 2.500 104.000 2.000; 1.000 18.250 2.440 113.000 9.000; 1.000 18.080 2.460 108.000 3.000; 1.000 14.600 2.560 96.000 11.000; 1.000 14.350 2.580 109.000 6.000; 1.000 17.620 2.530 90.000 6.000; 1.000 16.990 2.500 102.000 7.000; 1.000 17.720 2.450 96.000 6.000; 1.000 17.170 2.450 99.000 7.000; 1.000 17.100 2.360 92.000 1.000; 1.000 16.010 2.460 83.000 4.000; 1.000 17.040 2.430 95.000 4.000; 1.000 17.730 2.490 104.000 2.000; 1.000 15.280 2.480 100.000 8.000; 1.000 16.440 2.390 105.000 10.000; 1.000 16.700 2.580 95.000 8.000; 1.000 16.840 2.460 93.000 9.000; 1.000 17.710 2.380 115.000 5.000; 1.000 15.120 2.470 86.000 11.000; 1.000 16.780 2.520 99.000 7.000; 1.000 15.100 2.420 86.000 5.000; 1.000 16.060 2.510 88.000 6.000; 1.000 18.490 2.430 92.000 7.000; 1.000 16.700 2.610 102.000 11.000; 1.000 17.030 2.470 100.000 6.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 22815.1 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.thickness.CD.10.mgh --fsgd FSGD_CD.fsgd dods --C thickness_CD.mtx --surf fsaverage lh --cortex --glmdir lh.thickness_CD.glmdir 2. The FSGD file (if using one) 3. And the design matrix above From: Manish Dalwani To: Douglas Greve Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Monday, June 24, 2013 1:01 PM Subject: Re: [Freesurfer] Help with QDEC error Hi Nick and Doug, Can you suggest an alternative way if QDEC is unable to handle a single group? I would like to run these analyses to address reviewers comments. Best, Manish From: Douglas Greve To: Manish Dalwani Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, June 20, 2013 11:16 PM Subject: Re: [Freesurfer] Help with QDEC error I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug On 6/20/13 12:36 PM, Manish Dalwani wrote: Hi Doug and Freesurfers, > > >I realized that I hadn't updated my group levels to one group. However, when I >do that..the qdec complains about group.level having at minimum two levels. >How can I run (using QDEC) single group regression? > > >Thanks, >Manish > > > > > From: Manish Dalwani >To: Douglas Greve ; >"freesurfer@nmr.mgh.harvard.edu" >
Re: [Freesurfer] Help with QDEC error
Hi Nick and Doug, Can you suggest an alternative way if QDEC is unable to handle a single group? I would like to run these analyses to address reviewers comments. Best, Manish From: Douglas Greve To: Manish Dalwani Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, June 20, 2013 11:16 PM Subject: Re: [Freesurfer] Help with QDEC error I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug On 6/20/13 12:36 PM, Manish Dalwani wrote: Hi Doug and Freesurfers, > > >I realized that I hadn't updated my group levels to one group. However, when I >do that..the qdec complains about group.level having at minimum two levels. >How can I run (using QDEC) single group regression? > > >Thanks, >Manish > > > > > From: Manish Dalwani >To: Douglas Greve ; >"freesurfer@nmr.mgh.harvard.edu" >Sent: Thursday, June 20, 2013 1:26 PM >Subject: Re: [Freesurfer] Help with QDEC error > > > >Hi Doug, > > >I was out of town for a conference. Please see my attachments. I have the log >file and screenshots of ill-matrix conditioning. >Thanks for your help! >Manish > > > >____ > From: Douglas Greve >To: freesurfer@nmr.mgh.harvard.edu >Sent: Saturday, June 15, 2013 11:09 AM >Subject: Re: [Freesurfer] Help with QDEC error > > > > >Can you send the mri_glmfit.log file from >/Applications/freesurfer/subjects/qdec/Untitled ? >doug > > > >On 6/14/13 4:57 PM, Manish Dalwani wrote: > >Hello Freesurfers, >> >> >>I am trying to run regression analyses within patients and one variable of >>interest which adjusting for the nuisance variables age, IQ, thickness. When >>i select the group and the CD (variable of interest) and run analyses (DODS), >>I get the following error: >> >> >>Qdec 1.4 (Qdec1.4) >> >> >>Type: Error >>Time: Fri Jun 14 14:49:37 2013 >>Description: Error in Analyze: command failed: mri_glmfit --y >>/Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd >>/Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir >>/Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C >>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >> --C >>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat >> --C >>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat >> --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat >> >> >>Please advice! >> >> >>Regards, >>Manish Dalwani >>Instructor >>Dept. of Psychiatry >>University of Colorado >> >> >>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >___ >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 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 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] Help with QDEC error
I thought it would have worked with a single group. Maybe Nick knows of the top of his head. doug On 6/20/13 12:36 PM, Manish Dalwani wrote: Hi Doug and Freesurfers, I realized that I hadn't updated my group levels to one group. However, when I do that..the qdec complains about group.level having at minimum two levels. How can I run (using QDEC) single group regression? Thanks, Manish *From:* Manish Dalwani *To:* Douglas Greve ; "freesurfer@nmr.mgh.harvard.edu" *Sent:* Thursday, June 20, 2013 1:26 PM *Subject:* Re: [Freesurfer] Help with QDEC error Hi Doug, I was out of town for a conference. Please see my attachments. I have the log file and screenshots of ill-matrix conditioning. Thanks for your help! Manish *From:* Douglas Greve *To:* freesurfer@nmr.mgh.harvard.edu *Sent:* Saturday, June 15, 2013 11:09 AM *Subject:* Re: [Freesurfer] Help with QDEC error Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug On 6/14/13 4:57 PM, Manish Dalwani wrote: Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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] Help with QDEC error
Hi Doug and Freesurfers, I realized that I hadn't updated my group levels to one group. However, when I do that..the qdec complains about group.level having at minimum two levels. How can I run (using QDEC) single group regression? Thanks, Manish From: Manish Dalwani To: Douglas Greve ; "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, June 20, 2013 1:26 PM Subject: Re: [Freesurfer] Help with QDEC error Hi Doug, I was out of town for a conference. Please see my attachments. I have the log file and screenshots of ill-matrix conditioning. Thanks for your help! Manish From: Douglas Greve To: freesurfer@nmr.mgh.harvard.edu Sent: Saturday, June 15, 2013 11:09 AM Subject: Re: [Freesurfer] Help with QDEC error Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug On 6/14/13 4:57 PM, Manish Dalwani wrote: Hello Freesurfers, > > >I am trying to run regression analyses within patients and one variable of >interest which adjusting for the nuisance variables age, IQ, thickness. When i >select the group and the CD (variable of interest) and run analyses (DODS), I >get the following error: > > >Qdec 1.4 (Qdec1.4) > > >Type: Error >Time: Fri Jun 14 14:49:37 2013 >Description: Error in Analyze: command failed: mri_glmfit --y >/Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd >/Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir >/Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C >/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat > --C >/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat > --C >/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat > --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat > > >Please advice! > > >Regards, >Manish Dalwani >Instructor >Dept. of Psychiatry >University of Colorado > > >___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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 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] Help with QDEC error
Can you send the mri_glmfit.log file from /Applications/freesurfer/subjects/qdec/Untitled ? doug On 6/14/13 4:57 PM, Manish Dalwani wrote: Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] Help with QDEC error
Hello Freesurfers, I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error: Qdec 1.4 (Qdec1.4) Type: Error Time: Fri Jun 14 14:49:37 2013 Description: Error in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat --C /Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat Please advice! Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado___ 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.
