Thanks for the suggestion David. I tried it but I still got the same error :/
Gabriella
From: David Vazquez [mailto:dvazq002@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Gabriella.
I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us.
Good luck. -David
On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> wrote: Hi Freesurfer Experts,
I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format).
However, I am getting this error:
Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat
There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it?
Thank you! Gabriella
• Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
• Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hirsch, Gabriella" <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> Reply-To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq002@ucr.edumailto:dvazq002@ucr.edu> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec analysis with ICV
Thanks for the suggestion David. I tried it but I still got the same error :/
Gabriella
From: David Vazquez [mailto:dvazq002@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Gabriella.
I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us.
Good luck. -David
On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> wrote: Hi Freesurfer Experts,
I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format).
However, I am getting this error:
Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat
There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it?
Thank you! Gabriella
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
Hi Andrew, the values I'm using are already mean centered -- similarly, I've never been able to use the full ICV values. Even with David's suggestion of reducing the number of digits (effectively making the numbers smaller), it still doesn't work...
Gabriella
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 1:55 PM To: freesurfer@nmr.mgh.harvard.edu; David Vazquez Subject: Re: [Freesurfer] qdec analysis with ICV
Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hirsch, Gabriella" <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> Reply-To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq002@ucr.edumailto:dvazq002@ucr.edu> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec analysis with ICV
Thanks for the suggestion David. I tried it but I still got the same error :/
Gabriella
From: David Vazquez [mailto:dvazq002@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Gabriella.
I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us.
Good luck. -David
On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> wrote: Hi Freesurfer Experts,
I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format).
However, I am getting this error:
Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat
There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it?
Thank you! Gabriella
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
I believe your issue is you are trying to do a between group analysis but you only have 1 subject in group B. There is no way to estimate the variance in the measure if there is only one subject in the group. -Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hirsch, Gabriella" <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 13, 2015 at 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Andrew, the values I’m using are already mean centered -- similarly, I’ve never been able to use the full ICV values. Even with David’s suggestion of reducing the number of digits (effectively making the numbers smaller), it still doesn’t work…
Gabriella
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 1:55 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; David Vazquez Subject: Re: [Freesurfer] qdec analysis with ICV
Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hirsch, Gabriella" <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> Reply-To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq002@ucr.edumailto:dvazq002@ucr.edu> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec analysis with ICV
Thanks for the suggestion David. I tried it but I still got the same error :/
Gabriella
From: David Vazquez [mailto:dvazq002@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Gabriella.
I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us.
Good luck. -David
On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> wrote: Hi Freesurfer Experts,
I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format).
However, I am getting this error:
Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat
There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it?
Thank you! Gabriella
• Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
• Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
• Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not “Reply All.” After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
That does make sense Andrew. But would that be the case even if I weren't correcting for ICV? In other words, the analysis works when I don't correct for it. The GLM still looks for variance in group differences regardless if you're correcting for something or not...right?
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 4:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec analysis with ICV
I believe your issue is you are trying to do a between group analysis but you only have 1 subject in group B. There is no way to estimate the variance in the measure if there is only one subject in the group. -Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hirsch, Gabriella" <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 13, 2015 at 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Andrew, the values I'm using are already mean centered -- similarly, I've never been able to use the full ICV values. Even with David's suggestion of reducing the number of digits (effectively making the numbers smaller), it still doesn't work...
Gabriella
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew Sent: Friday, November 13, 2015 1:55 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; David Vazquez Subject: Re: [Freesurfer] qdec analysis with ICV
Try mean centering your ICV values (I.e. Subtract the mean value from each individual value). This has worked for me to bypass this error. -Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Hirsch, Gabriella" <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> Reply-To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq002@ucr.edumailto:dvazq002@ucr.edu> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] qdec analysis with ICV
Thanks for the suggestion David. I tried it but I still got the same error :/
Gabriella
From: David Vazquez [mailto:dvazq002@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV
Hi Gabriella.
I'm not an expert, but I've had this problem too. Reduce the number of digits for ICV by converting it be cm^3 instead of mm^3. Also get rid of some decimal places. It works for us.
Good luck. -David
On Fri, Nov 13, 2015, 8:10 AM Hirsch, Gabriella <Gabriella_Hirsch@meei.harvard.edumailto:Gabriella_Hirsch@meei.harvard.edu> wrote: Hi Freesurfer Experts,
I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the .dat extension as my email server didn't like the dat format).
However, I am getting this error:
Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 1.000 0.000 -28915.199; 0.000 1.000 0.000 194736.703; 0.000 1.000 0.000 -184311.000; 1.000 0.000 18489.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- 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 /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh --fsgd /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd dods --glmdir /media/seagate_external_/freesurfer_subjects/qdec/Untitled --surf fsaverage rh --label /media/seagate_external_/freesurfer_subjects/fsaverage/label/rh.aparc.label --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Avg-volume-ICV-Cor.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Intercept-volume.mat --C /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/rh-Diff-CVI-PVL-Cor-volume-ICV.mat
There are no duplicate entries. I have done this same analysis with a higher number of subjects without problems. I have also tried using the inbuilt qdec ICV (which is not demeaned) and got the same error. Could this be a problem with the small subject count? If so, is there any way to remedy it?
Thank you! Gabriella
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
* Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.
freesurfer@nmr.mgh.harvard.edu
-
Hirsch, Gabriella -
O'Shea,Andrew