External Email - Use Caution
Hello FreeSurfer Developers,
I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1.
I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat.
So I tried to put those to terminal, the feedback is:
gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you
Best regards
Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and upload it here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/9/19 6:35 AM, Abby tang wrote:
External Email - Use Caution
Hello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat
sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or QDEC.tar.gz. Thank you.
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年7月9日周二 下午10:42写道：
Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and upload it here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/9/19 6:35 AM, Abby tang wrote:
External Email - Use CautionHello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat.
So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat
sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Greve Can you download those files? I have uploaded it in ftp, the file name is QDEC.tar.gz. Hope you can help me. Thank you very much. Abby
Abby tang abbytang0925@gmail.com 于2019年7月10日周三 上午9:46写道：
Hi I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or QDEC.tar.gz. Thank you.
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年7月9日周二 下午10:42写道：
Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and upload it here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/9/19 6:35 AM, Abby tang wrote:
External Email - Use CautionHello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat.
So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat
sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to
/home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat
Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see the file there, but it has zero length. Check whether your source file actually has something in it. If it does, try uploading it again (you may have to use a different file name)
On 7/10/2019 9:17 PM, Abby tang wrote:
External Email - Use Caution
Hi Greve Can you download those files? I have uploaded it in ftp, the file name is QDEC.tar.gz. Hope you can help me. Thank you very much. Abby
Abby tang <abbytang0925@gmail.commailto:abbytang0925@gmail.com> 于2019年7月10日周三 上午9:46写道： Hi I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or QDEC.tar.gz. Thank you.
Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> 于2019年7月9日周二 下午10:42写道： Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and upload it here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/9/19 6:35 AM, Abby tang wrote:
External Email - Use CautionHello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat. So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat --C /home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat
sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to /home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132, fwhm=14.256391 Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Greve Can you download those files? I have uploaded it in ftp website and send to your email, the file name is Untitled.rar. Hope you can help me. Thank you very much. Abby
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年7月15日周一 下午12:07写道：
I see the file there, but it has zero length. Check whether your source file actually has something in it. If it does, try uploading it again (you may have to use a different file name)
On 7/10/2019 9:17 PM, Abby tang wrote:
External Email - Use CautionHi Greve Can you download those files? I have uploaded it in ftp, the file name is QDEC.tar.gz. Hope you can help me. Thank you very much. Abby
Abby tang abbytang0925@gmail.com 于2019年7月10日周三 上午9:46写道：
Hi I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or QDEC.tar.gz. Thank you.
Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 于2019年7月9日周二 下午10:42写道：
Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and upload it here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is
On 7/9/19 6:35 AM, Abby tang wrote:
External Email - Use CautionHello FreeSurfer Developers, I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV, so QDEC was used. However I met a problem when I use it, such as picture1. I get the wrong message, Error in Analyze: command failed: mri_glmfit --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat.
So I tried to put those to terminal, the feedback is: gdfRead(): reading /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 80.3537 2.43637 1 education 12.189 3.6099 2 eTIV 1.33934e+06 242446 Class Means of each Continuous Variable 1 sexFemale 80.0568 11.4773 1265564.4638 2 sexMale 80.6974 13.0132 1424768.7681 INFO: gd2mtx_method is dods Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/abby/Desktop/qdecyoung/qdec cmdline mri_glmfit.bin --y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh --fsgd /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd dods --glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled --surf fsaverage lh --label /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label --C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Intercept-thickness.mat
--C
/home/abby/Desktop/qdecyoung/qdec/Untitled/contrasts/lh-Diff-Female-Male-Cor-thickness-age.mat
sysname Linux hostname abby-virtual-machine machine x86_64 user abby FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /home/abby/Desktop/qdecyoung/qdec/Untitled/qdec.fsgd labelmask /home/abby/Desktop/qdecyoung/fsaverage/label/lh.aparc.label maskinv 0 glmdir /home/abby/Desktop/qdecyoung/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/abby/Desktop/qdecyoung/qdec/Untitled Loading y from /home/abby/Desktop/qdecyoung/qdec/Untitled/y.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to
/home/abby/Desktop/qdecyoung/qdec/Untitled/Xg.dat
Computing normalized matrix Normalized matrix condition is 9294.65 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 1.175494e-38 Found 139197 voxels in mask Saving mask to /home/abby/Desktop/qdecyoung/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 69257.619818 DOF = 156 Starting fit and test Fit completed in 0.338183 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995542, ar1std=0.000996, gstd=6.054132,
fwhm=14.256391
Writing results lh-Avg-Intercept-thickness maxvox sig=10.0394 F=48.3686 at index 13210 0 0 seed=1563457975 MatrixMultiplyD(): m2 is null break matrix.c:415
No such file or directory
When same operations were did with other files, Qdec running normally. I don't know why. Please help me. Thank you Best regards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Abby tang -
Greve, Douglas N.,Ph.D.