Those are the qdec tables, not the fsgd file. Look in the qdec output folder for a file called y.fsgd. Also please remember to post to the list and not to us personally
On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote:
External Email - Use Caution
Hi Doug,
Thank you for your reply.
I send my FSGD files. sui3_qdec.table sui5_qdec.table - This file contains the normalization of SSI score (nrSSI).
I want to see the correlation (or regression) between the brain surface areas with significant difference between two groups and SSI score. When I enter 'SSI' or 'nrSSI' into covariate in QDEC, then error occurs.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
ᐧ
2018년 6월 15일 (금) 오전 12:26, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>님이 작성:
Please send the y.fsgd file On 06/13/2018 09:30 PM, Seung-Gul Kang (강승걸) wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I send you this e-mail again in anticipation of your help. > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > sysnameLinux > > hostname localhost.localdomain > > machinex86_64 > > usersgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing1 > > OneSampleGroupMean 0 > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > logyflag 0 > > usedti0 > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > Normalized matrix condition is 24522.5 > > Design matrix ------------------ > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > -------------------------------- > > 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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Error in Analyze: command failed: mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > I also attach the error message. > > Could you tell me how I can fix this problem? > > I am sincerely looking forward to receiving your reply. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ---------- Forwarded message --------- > From: Seung-Gul Kang (강승걸) <sg.kang422@gmail.com <mailto:sg.kang422@gmail.com> > <mailto:sg.kang422@gmail.com <mailto:sg.kang422@gmail.com>>> > Date: 2018년 6월 12일 (화) 오후 3:32 > Subject: Error during QDEC > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Dear Freesurfer experts, > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > sysnameLinux > > hostname localhost.localdomain > > machinex86_64 > > usersgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing1 > > OneSampleGroupMean 0 > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > logyflag 0 > > usedti0 > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > Normalized matrix condition is 24522.5 > > Design matrix ------------------ > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > -------------------------------- > > 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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Error in Analyze: command failed: mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > I also attach the error message. > > Could you tell me how I can fix this problem? > > I am looking forward to receiving your reply. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ᐧ > ᐧ 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.
External Email - Use Caution
Dear Dr. Douglas Greve,
I am sorry for the the wrong file and also sorry if you have any inconvenience.
Strange to say, I could not find y.fsgd file. Perhaps the file was not be created due to an error.
Instead, I send the file folder which was generated after qdec. It contains the qdec.fsgd file. (I could not send y.mgh file due to capacity limit.)
Thank you.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
2018년 6월 15일 (금) 오후 10:47, Douglas Greve dgreve@mgh.harvard.edu님이 작성:
Those are the qdec tables, not the fsgd file. Look in the qdec output folder for a file called y.fsgd. Also please remember to post to the list and not to us personally
On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote:
External Email - Use CautionHi Doug,
Thank you for your reply.
I send my FSGD files. sui3_qdec.table sui5_qdec.table - This file contains the normalization of SSI score (nrSSI).
I want to see the correlation (or regression) between the brain surface areas with significant difference between two groups and SSI score. When I enter 'SSI' or 'nrSSI' into covariate in QDEC, then error occurs.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
ᐧ
2018년 6월 15일 (금) 오전 12:26, Douglas N. Greve dgreve@mgh.harvard.edu님이 작성:
Please send the y.fsgd file
On 06/13/2018 09:30 PM, Seung-Gul Kang (강승걸) wrote:
External Email - Use CautionDear Freesurfer experts,
I send you this e-mail again in anticipation of your help.
I see the error message when I perform QDEC. The error message is as below.
Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/sgk
cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
sysnameLinux
hostname localhost.localdomain
machinex86_64
usersgk
FixVertexAreaFlag = 1
UseMaskWithSmoothing1
OneSampleGroupMean 0
y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
logyflag 0
usedti0
FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd
labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI
Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat
Normalized matrix condition is 24522.5
Design matrix ------------------
1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000;
1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000;
1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000;
0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000;
0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000;
0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000;
1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000;
0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000;
0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000;
0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000;
1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000;
1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000;
1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000;
1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000;
1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000;
1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000;
1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000;
0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000;
0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000;
0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094;
0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000;
0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203;
0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297;
0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000;
0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000;
0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500;
0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000;
0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094;
0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500;
0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000;
0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797;
0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000;
0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297;
0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000;
0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000;
0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406;
0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203;
0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000;
ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5
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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
The FSGD file (if using one)
And the design matrix above
Error in Analyze: command failed: mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
I also attach the error message.
Could you tell me how I can fix this problem?
I am sincerely looking forward to receiving your reply.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
---------- Forwarded message --------- From: Seung-Gul Kang (강승걸) <sg.kang422@gmail.com mailto:sg.kang422@gmail.com> Date: 2018년 6월 12일 (화) 오후 3:32 Subject: Error during QDEC To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Dear Freesurfer experts,
I see the error message when I perform QDEC. The error message is as below.
Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/sgk
cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
sysnameLinux
hostname localhost.localdomain
machinex86_64
usersgk
FixVertexAreaFlag = 1
UseMaskWithSmoothing1
OneSampleGroupMean 0
y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
logyflag 0
usedti0
FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd
labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
maskinv 0
glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI
Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh
INFO: gd2mtx_method is dods
Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat
Normalized matrix condition is 24522.5
Design matrix ------------------
1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000;
1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000;
1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000;
0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000;
0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000;
0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000;
1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000;
0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000;
0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000;
0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000;
1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000;
1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000;
1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000;
1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000;
1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000;
1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000;
1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000;
0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000;
0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000;
0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094;
0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000;
0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203;
0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297;
0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000;
0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000;
0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500;
0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000;
0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094;
0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500;
0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000;
0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797;
0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000;
0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297;
0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000;
0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000;
0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406;
0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203;
0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000;
ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5
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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
The FSGD file (if using one)
And the design matrix above
Error in Analyze: command failed: mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
--C
/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
I also attach the error message.
Could you tell me how I can fix this problem?
I am looking forward to receiving your reply.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
ᐧ ᐧ
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.
ᐧ
Sorry, it was the qdec.fsgd file that I was looking for. Based on that, I would say that you are having a scaling problem. The "AREA" column has a scale that is much larger than the other columns. I would recommend that you normalize the values (ie, subtract the mean and divide by the sqrt of the sum of the squares)
On 06/15/2018 06:50 PM, Seung-Gul Kang (강승걸) wrote:
Dear Dr. Douglas Greve,
I am sorry for the the wrong file and also sorry if you have any inconvenience.
Strange to say, I could not find y.fsgd file. Perhaps the file was not be created due to an error.
Instead, I send the file folder which was generated after qdec. It contains the qdec.fsgd file. (I could not send y.mgh file due to capacity limit.)
Thank you.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
2018년 6월 15일 (금) 오후 10:47, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>님이 작성:
Those are the qdec tables, not the fsgd file. Look in the qdec output folder for a file called y.fsgd. Also please remember to post to the list and not to us personally On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote:External Email - Use Caution Hi Doug, Thank you for your reply. I send my FSGD files. sui3_qdec.table sui5_qdec.table - This file contains the normalization of SSI score (nrSSI). I want to see the correlation (or regression) between the brain surface areas with significant difference between two groups and SSI score. When I enter 'SSI' or 'nrSSI' into covariate in QDEC, then error occurs. Best regards, Seung-Gul *S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea ᐧ 2018년 6월 15일 (금) 오전 12:26, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>님이 작성: Please send the y.fsgd file On 06/13/2018 09:30 PM, Seung-Gul Kang (강승걸) wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I send you this e-mail again in anticipation of your help. > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > sysnameLinux > > hostname localhost.localdomain > > machinex86_64 > > usersgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing1 > > OneSampleGroupMean 0 > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > logyflag 0 > > usedti0 > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > Normalized matrix condition is 24522.5 > > Design matrix ------------------ > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > -------------------------------- > > 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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Error in Analyze: command failed: mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > I also attach the error message. > > Could you tell me how I can fix this problem? > > I am sincerely looking forward to receiving your reply. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ---------- Forwarded message --------- > From: Seung-Gul Kang (강승걸) <sg.kang422@gmail.com <mailto:sg.kang422@gmail.com> > <mailto:sg.kang422@gmail.com <mailto:sg.kang422@gmail.com>>> > Date: 2018년 6월 12일 (화) 오후 3:32 > Subject: Error during QDEC > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Dear Freesurfer experts, > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > sysnameLinux > > hostname localhost.localdomain > > machinex86_64 > > usersgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing1 > > OneSampleGroupMean 0 > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > logyflag 0 > > usedti0 > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > > labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label > > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > Normalized matrix condition is 24522.5 > > Design matrix ------------------ > > 1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000; > > 1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000; > > 1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000; > > 0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000; > > 0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000; > > 1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000; > > 0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000; > > 0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000; > > 1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000; > > 1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000; > > 1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000; > > 1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000; > > 1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000; > > 1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000; > > 0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000; > > 0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000; > > 0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094; > > 0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297; > > 0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000; > > 0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500; > > 0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094; > > 0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500; > > 0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000; > > 0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797; > > 0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297; > > 0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000; > > 0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000; > > 0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406; > > 0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203; > > 0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000; > > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > -------------------------------- > > 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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Error in Analyze: command failed: mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat > --C > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat > > I also attach the error message. > > Could you tell me how I can fix this problem? > > I am looking forward to receiving your reply. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ᐧ > ᐧ 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.ᐧ
External Email - Use Caution
Dear Dr. Greve,
Thank you so much for your help!
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
ᐧ
2018년 6월 19일 (화) 오전 2:43, Douglas N. Greve dgreve@mgh.harvard.edu님이 작성:
Sorry, it was the qdec.fsgd file that I was looking for. Based on that, I would say that you are having a scaling problem. The "AREA" column has a scale that is much larger than the other columns. I would recommend that you normalize the values (ie, subtract the mean and divide by the sqrt of the sum of the squares)
On 06/15/2018 06:50 PM, Seung-Gul Kang (강승걸) wrote:
Dear Dr. Douglas Greve,
I am sorry for the the wrong file and also sorry if you have any inconvenience.
Strange to say, I could not find y.fsgd file. Perhaps the file was not be created due to an error.
Instead, I send the file folder which was generated after qdec. It contains the qdec.fsgd file. (I could not send y.mgh file due to capacity limit.)
Thank you.
Best regards, Seung-Gul
*S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center 연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea
2018년 6월 15일 (금) 오후 10:47, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>님이 작성:
Those are the qdec tables, not the fsgd file. Look in the qdec output folder for a file called y.fsgd. Also please remember to post to the list and not to us personally On 6/15/18 12:40 AM, Seung-Gul Kang (강승걸) wrote:External Email - Use Caution Hi Doug, Thank you for your reply. I send my FSGD files. sui3_qdec.table sui5_qdec.table - This file contains the normalization of SSI score (nrSSI). I want to see the correlation (or regression) between the brain surface areas with significant difference between two groups and SSI score. When I enter 'SSI' or 'nrSSI' into covariate in QDEC, then error occurs. Best regards, Seung-Gul *S**eung-Gul Kang, M.D., Ph.D. * Psychiatrist, Professor; Department of Psychiatry, Gil MedicalCenter
연구부학장. Dean, Department of Research Affairs; Gachon University College of Medicine 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea ᐧ 2018년 6월 15일 (금) 오전 12:26, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>님이 작성: Please send the y.fsgd file On 06/13/2018 09:30 PM, Seung-Gul Kang (강승걸) wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I send you this e-mail again in anticipation of your help. > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
> > sysnameLinux > > hostname localhost.localdomain > > machinex86_64 > > usersgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing1 > > OneSampleGroupMean 0 > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > logyflag 0 > > usedti0 > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > >labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
> > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > Normalized matrix condition is 24522.5 > > Design matrix ------------------ > >1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000;
> >1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000;
> >1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000;
> >0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000;
> >0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000;
> >0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000;
> >1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000;
> >0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000;
> >0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000;
> >0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000;
> >1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000;
> >1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000;
> >1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000;
> >1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000;
> >1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000;
> >1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000;
> >1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000;
> >0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000;
> >0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000;
> >0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094;
> >0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000;
> >0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203;
> >0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297;
> >0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000;
> >0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000;
> >0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500;
> >0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000;
> >0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094;
> >0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500;
> >0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000;
> >0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797;
> >0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000;
> >0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297;
> >0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000;
> >0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000;
> >0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406;
> >0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203;
> >0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000;
> > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > -------------------------------- > > 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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
> > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Error in Analyze: command failed: mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
> > I also attach the error message. > > Could you tell me how I can fix this problem? > > I am sincerely looking forward to receiving your reply. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ---------- Forwarded message --------- > From: Seung-Gul Kang (강승걸) <sg.kang422@gmail.com <mailto:sg.kang422@gmail.com> > <mailto:sg.kang422@gmail.com <mailto:sg.kang422@gmail.com>>> > Date: 2018년 6월 12일 (화) 오후 3:32 > Subject: Error during QDEC > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Dear Freesurfer experts, > > I see the error message when I perform QDEC. > The error message is as below. > > Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ > > cwd /home/sgk > > cmdline mri_glmfit --y /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > --fsgd /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods > --glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh > --label /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
>/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
> > > sysnameLinux > > hostname localhost.localdomain > > machinex86_64 > > usersgk > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing1 > > OneSampleGroupMean 0 > > y/mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > logyflag 0 > > usedti0 > > FSGD /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd > >labelmask/mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label
> > maskinv 0 > > glmdir /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory /mnt/hgfs/share/suicide/qdec/LH_area_SSI > > Loading y from /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh > > INFO: gd2mtx_method is dods > > Saving design matrix to /mnt/hgfs/share/suicide/qdec/LH_area_SSI/Xg.dat > > Normalized matrix condition is 24522.5 > > Design matrix ------------------ > >1.0000.0000.0000.00015.0000.0000.0000.00024.0000.0000.0000.00021.0000.0000.0000.000149457.5940.0000.0000.000;
> >1.0000.0000.0000.00019.0000.0000.0000.00050.0000.0000.0000.00020.0000.0000.0000.000161540.2030.0000.0000.000;
> >1.0000.0000.0000.0007.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000167295.9060.0000.0000.000;
> >0.0000.0001.0000.0000.0000.00010.0000.0000.0000.00031.0000.0000.0000.00027.0000.0000.0000.000175241.7030.000;
> >0.0000.0001.0000.0000.0000.00015.0000.0000.0000.00059.0000.0000.0000.00023.0000.0000.0000.000165616.7970.000;
> >0.0000.0001.0000.0000.0000.00011.0000.0000.0000.00057.0000.0000.0000.00022.0000.0000.0000.000183255.5940.000;
> >1.0000.0000.0000.00026.0000.0000.0000.00037.0000.0000.0000.00023.0000.0000.0000.000159212.2030.0000.0000.000;
> >0.0000.0001.0000.0000.0000.00014.0000.0000.0000.00050.0000.0000.0000.00022.0000.0000.0000.000170017.0940.000;
> >0.0000.0001.0000.0000.0000.00016.0000.0000.0000.00026.0000.0000.0000.00019.0000.0000.0000.000190217.9060.000;
> >0.0000.0001.0000.0000.0000.0001.0000.0000.0000.00039.0000.0000.0000.00019.0000.0000.0000.000156341.0000.000;
> >1.0000.0000.0000.00018.0000.0000.0000.00049.0000.0000.0000.00032.0000.0000.0000.000168844.2970.0000.0000.000;
> >1.0000.0000.0000.00021.0000.0000.0000.00039.0000.0000.0000.00026.0000.0000.0000.000149945.4060.0000.0000.000;
> >1.0000.0000.0000.00011.0000.0000.0000.00039.0000.0000.0000.00022.0000.0000.0000.000166132.9060.0000.0000.000;
> >1.0000.0000.0000.00017.0000.0000.0000.00041.0000.0000.0000.00025.0000.0000.0000.000139924.4060.0000.0000.000;
> >1.0000.0000.0000.00027.0000.0000.0000.00045.0000.0000.0000.00034.0000.0000.0000.000133331.7970.0000.0000.000;
> >1.0000.0000.0000.00011.0000.0000.0000.00047.0000.0000.0000.00024.0000.0000.0000.000164844.7030.0000.0000.000;
> >1.0000.0000.0000.00023.0000.0000.0000.00046.0000.0000.0000.00026.0000.0000.0000.000163024.2030.0000.0000.000;
> >0.0000.0001.0000.0000.0000.00031.0000.0000.0000.00042.0000.0000.0000.00033.0000.0000.0000.000140203.7970.000;
> >0.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00029.0000.0000.0000.000186282.2970.000;
> >0.0000.0000.0001.0000.0000.0000.00018.0000.0000.0000.00021.0000.0000.0000.00017.0000.0000.0000.000171746.094;
> >0.0001.0000.0000.0000.00017.0000.0000.0000.00034.0000.0000.0000.00015.0000.0000.0000.000145005.2030.0000.000;
> >0.0000.0000.0001.0000.0000.0000.00015.0000.0000.0000.00054.0000.0000.0000.00027.0000.0000.0000.000168633.203;
> >0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00027.0000.0000.0000.00020.0000.0000.0000.000186731.297;
> >0.0001.0000.0000.0000.0001.0000.0000.0000.00061.0000.0000.0000.00028.0000.0000.0000.000154627.5000.0000.000;
> >0.0001.0000.0000.0000.00010.0000.0000.0000.00044.0000.0000.0000.00022.0000.0000.0000.000154626.2970.0000.000;
> >0.0000.0000.0001.0000.0000.0000.0004.0000.0000.0000.00059.0000.0000.0000.00020.0000.0000.0000.000177918.500;
> >0.0001.0000.0000.0000.0004.0000.0000.0000.00056.0000.0000.0000.00027.0000.0000.0000.000157687.7970.0000.000;
> >0.0000.0000.0001.0000.0000.0000.0008.0000.0000.0000.00058.0000.0000.0000.00032.0000.0000.0000.000173899.094;
> >0.0000.0000.0001.0000.0000.0000.00021.0000.0000.0000.00020.0000.0000.0000.00018.0000.0000.0000.000175980.500;
> >0.0001.0000.0000.0000.0000.0000.0000.0000.00059.0000.0000.0000.00028.0000.0000.0000.000162526.7030.0000.000;
> >0.0000.0000.0001.0000.0000.0000.0002.0000.0000.0000.00037.0000.0000.0000.00020.0000.0000.0000.000198622.797;
> >0.0001.0000.0000.0000.0003.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000157633.9060.0000.000;
> >0.0000.0000.0001.0000.0000.0000.00017.0000.0000.0000.00021.0000.0000.0000.00021.0000.0000.0000.000164236.297;
> >0.0001.0000.0000.0000.00022.0000.0000.0000.00046.0000.0000.0000.00023.0000.0000.0000.000144559.7030.0000.000;
> >0.0001.0000.0000.0000.0007.0000.0000.0000.00032.0000.0000.0000.00024.0000.0000.0000.000156151.5000.0000.000;
> >0.0000.0000.0001.0000.0000.0000.00016.0000.0000.0000.00046.0000.0000.0000.00027.0000.0000.0000.000154306.406;
> >0.0000.0000.0001.0000.0000.0000.0000.0000.0000.0000.00019.0000.0000.0000.00020.0000.0000.0000.000188334.203;
> >0.0001.0000.0000.0000.00020.0000.0000.0000.00055.0000.0000.0000.00026.0000.0000.0000.000134977.4060.0000.000;
> > -------------------------------- > > ERROR: matrix is ill-conditioned or badly scaled, condno = 24522.5 > > -------------------------------- > > 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 /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
>/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat--C
>/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
> > > 2. The FSGD file (if using one) > > 3. And the design matrix above > > Error in Analyze: command failed: mri_glmfit --y > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/y.mgh --fsgd > /mnt/hgfs/share/suicide/qdec/LH_area_SSI/qdec.fsgd dods --glmdir > /mnt/hgfs/share/suicide/qdec/LH_area_SSI --surf fsaverage lh --label > /mnt/hgfs/share/suicide/fsaverage/label/lh.aparc.label --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Avg-area-SSI-Cor.mat--C
>/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-S-NS-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-Diff-F-M-Cor-area-SSI.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Intercept-area.mat
> --C >/mnt/hgfs/share/suicide/qdec/LH_area_SSI/contrasts/lh-X-diagnosis-sex-Cor-area-SSI.mat
> > I also attach the error message. > > Could you tell me how I can fix this problem? > > I am looking forward to receiving your reply. > > Best regards, > Seung-Gul > > *S**eung-Gul Kang, M.D., Ph.D. * > Psychiatrist, Professor; Department of Psychiatry, Gil Medical Center > 연구부학장. Dean, Department of Research Affairs; Gachon University > College of Medicine > 인천광역시자살예방센터장. Director, Incheon Suicide Prevention Center > 21, Namdong-daero 774 beon-gil, Namdong-gu, Incheon, 21565, South Korea > > ᐧ > ᐧ 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.ᐧ
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N. Greve
-
Seung-Gul Kang (강승걸)