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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Hirsch, Gabriella" <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> Reply-To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, November 13, 2015 at 1:03 PM To: David Vazquez <dvazq...@ucr.edu<mailto:dvazq...@ucr.edu>> Cc: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto: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:dvazq...@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_hir...@meei.harvard.edu<mailto:gabriella_hir...@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.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. * 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 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.
