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
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
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 greve@nmr.mgh.harvard.edu 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.
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 manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu 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.
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 manishdalwani@yahoo.com *To:* Douglas Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu *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.
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 greve@nmr.mgh.harvard.edu To: Manish Dalwani manishdalwani@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" 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 manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu 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
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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 manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu To: Manish Dalwani manishdalwani@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" 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 manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu 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
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Compliance HelpLine at
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Hello Doug,
I was able to make it work after removing mean thickness from the model. It may have a positive association with age which led to ill matrix conditioning.
Manish
________________________________ From: Manish Dalwani manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, June 25, 2013 2:20 PM Subject: 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 manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu Cc: "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu To: Manish Dalwani manishdalwani@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" 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 manishdalwani@yahoo.com To: Douglas Greve greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu 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
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Compliance HelpLine at
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_______________________________________________ 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.
Hi Manish, sorry for the delay. Ithink the problem is that there is almost no range in the thickness measures which makes that column nearly identical toa column of all ones. You can try demeaning the thickness. doug
On 06/25/2013 04:20 PM, Manish Dalwani wrote:
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:
- 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 manishdalwani@yahoo.com *To:* Douglas Greve greve@nmr.mgh.harvard.edu *Cc:* "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu *To:* Manish Dalwani manishdalwani@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" 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 manishdalwani@yahoo.com mailto:manishdalwani@yahoo.com *To:* Douglas Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu mailto: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.
Thanks for that email Doug, I will try that option!
Sent from my iPhone
On Jul 8, 2013, at 12:41 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Manish, sorry for the delay. Ithink the problem is that there is almost no range in the thickness measures which makes that column nearly identical toa column of all ones. You can try demeaning the thickness. doug
On 06/25/2013 04:20 PM, Manish Dalwani wrote:
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:
- 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 manishdalwani@yahoo.com *To:* Douglas Greve greve@nmr.mgh.harvard.edu *Cc:* "freesurfer@nmr.mgh.harvard.edu" 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 greve@nmr.mgh.harvard.edu *To:* Manish Dalwani manishdalwani@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" 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 manishdalwani@yahoo.com mailto:manishdalwani@yahoo.com *To:* Douglas Greve greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu mailto: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
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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. 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.
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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 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Manish Dalwani