Hi Nick,
Thanks for responding. We found a solution to the issue with the SUBJECTS_DIR (which was pointing to the location of our data, not the FS installation). This issue appeared after doing some software updates on our cluster (including Ubuntu). Here is how we fixed it:
sudo mv /bin/sh /bin/sh.orig sudo ln -s /bin/bash /bin/sh
However, once we got that issue fixed, we've been having another issue that we haven't been able to resolve. I would love any thoughts you have. The data table loads successfully, it reads in the correct number of discrete and continuous factors and can find all the subjects. However, when we go to analyze the data, we get an error in the terminal that says: ERROR: QdecGlmDesign::Create: zero factors!
I can't find any information about this in the archive and am stumped as to what is going on. Do you have any thoughts?
Many thanks! Kate
Full output here:
Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42
Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data..........................................Subject verification complete. Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 0.000000 0.763636 0.000000 0.000000 1.500000 -3.547619 348130.000000 2 1014 0.000000 0.098336 0.000000 0.000000 -11.500000 -10.547619 149370.000000 3 1032 0.000000 2.507636 0.000000 0.000000 2.500000 0.452381 -960.000000 4 1034 0.000000 0.101136 0.000000 0.000000 -15.500000 -11.547619 190570.000000 5 1041 1.000000 -2.516264 0.000000 1.000000 17.500000 12.452381 -26620.000000 6 1043 1.000000 -1.453964 0.000000 0.000000 7.500000 12.452381 205250.000000 7 1047 0.000000 -0.933764 0.000000 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 1.000000 1.171636 1.000000 0.000000 14.500000 7.452381 -42730.000000 9 1077 0.000000 0.281836 1.000000 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 1.000000 0.142136 1.000000 0.000000 3.500000 -1.547619 -158930.000000 11 1096 0.000000 -1.711364 1.000000 0.000000 -6.500000 -6.547619 31690.000000 12 1097 0.000000 -0.323264 1.000000 0.000000 6.500000 0.452381 -218300.000000 13 1099 0.000000 2.488536 0.000000 0.000000 -14.500000 -8.547619 279160.000000 14 1100 1.000000 1.404336 1.000000 0.000000 9.500000 -0.547619 -77570.000000 15 1114 1.000000 -0.312264 1.000000 0.000000 -10.500000 -12.547619 141560.000000 16 1119 1.000000 -1.374564 0.000000 0.000000 -7.500000 18.452381 110660.000000 17 1123 1.000000 0.988136 0.000000 0.000000 33.500000 16.452381 -27400.000000 18 1125 0.000000 0.287236 1.000000 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 0.000000 -1.820864 0.000000 0.000000 -14.500000 -12.547619 348770.000000 20 1128 0.000000 -1.338964 1.000000 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 0.000000 -2.086464 1.000000 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 1.000000 1.324936 0.000000 0.000000 12.500000 23.452381 -108080.000000 23 1139 1.000000 0.875936 1.000000 0.000000 -4.500000 0.452381 -199980.000000 24 1142 1.000000 -0.851664 1.000000 0.000000 10.500000 2.452381 -386850.000000 25 1143 1.000000 -2.820164 1.000000 0.000000 11.500000 -13.547619 -109600.000000 26 1153 1.000000 -2.458764 1.000000 0.000000 13.500000 10.452381 369170.000000 27 1154 1.000000 -1.234964 1.000000 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 0.000000 1.034736 1.000000 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 1.000000 1.163436 1.000000 0.000000 11.500000 11.452381 -71900.000000 30 1163 1.000000 1.371436 0.000000 0.000000 15.500000 7.452381 239550.000000 31 1165 1.000000 -0.517664 0.000000 1.000000 -11.500000 -2.547619 16810.000000 32 1166 1.000000 -2.302764 0.000000 1.000000 -7.500000 1.452381 220140.000000 33 1167 1.000000 0.292736 1.000000 1.000000 12.500000 11.452381 -117810.000000 34 1171 0.000000 1.385136 1.000000 0.000000 6.500000 -7.547619 59040.000000 35 1173 0.000000 1.075736 1.000000 0.000000 -7.500000 2.452381 -86380.000000 36 1175 0.000000 1.765736 1.000000 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 0.000000 1.732836 0.000000 0.000000 -11.500000 -3.547619 108560.000000 38 1177 1.000000 0.717136 1.000000 0.000000 -5.500000 10.452381 -53070.000000 39 1178 1.000000 -0.241164 1.000000 0.000000 33.500000 15.452381 -110020.000000 40 1179 0.000000 0.944336 1.000000 0.000000 -7.500000 0.452381 15300.000000 41 1180 0.000000 0.760936 1.000000 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 0.000000 -0.380764 1.000000 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment continuous 0 2 age_demean continuous 0 3 sex continuous 0 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- maltreatment 0.500 0.506 age_demean -0.000 1.410 sex 0.619 0.492 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248
Number of subjects: 42 Number of factors: 7 (0 discrete, 7 continuous) Number of classes: 1 Number of regressors: 8 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' ERROR: QdecGlmDesign::Create: zero factors!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [nicks@nmr.mgh.harvard.edu] Sent: Monday, August 11, 2014 2:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] error loading subjects in QDEC
Katie,
Hi, is the SUBJECTS_DIR set to the proper directory? I see from the output that it is set to:
SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3'
which seems to imply that it might be set to the location of your freesurfer installation, and not the location of the subject data (the directory where '1009', '1014', etc. are found).
N.
On Tue, 2014-08-05 at 23:07 +0000, McLaughlin, Katie wrote:
Hi Nick et al,
Just wanted to follow up on this. It seems as though Nick Schmansky has worked through this issue with previous FS users who have had the same error.
We are having an issue with QDEC recognizing subjects in the SUBJECTS_DIR. It is not a permissions issue (777 for all) and all the subjects are in the directory following recon-all and the qcache completed. The data table loads but cannot find any of the subjects. Data table was created in Linux.
Nick - we have searched through the archives and haven't found a solution to this issue, although a number of other users have had the same problem. I'm wondering if you've found a solution?
Many thanks, Kate
Error Output:
Reading /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/tktools/tkUtils.tcl
Using /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/lib/tcl/fsgdfPlot.tcl
Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42
Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR Too many subjects not found! Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 0.763636 m 0.000000 1.500000 -3.547619 348130.000000 2 1014 c 0.098336 m 0.000000 -11.500000 -10.547619 149370.000000 3 1032 c 2.507636 m 0.000000 2.500000 0.452381 -960.000000 4 1034 c 0.101136 m 0.000000 -15.500000 -11.547619 190570.000000 5 1041 m -2.516264 m 1.000000 17.500000 12.452381 -26620.000000 6 1043 m -1.453964 m 0.000000 7.500000 12.452381 205250.000000 7 1047 c -0.933764 m 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 m 1.171636 f 0.000000 14.500000 7.452381 -42730.000000 9 1077 c 0.281836 f 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 m 0.142136 f 0.000000 3.500000 -1.547619 -158930.000000 11 1096 c -1.711364 f 0.000000 -6.500000 -6.547619 31690.000000 12 1097 c -0.323264 f 0.000000 6.500000 0.452381 -218300.000000 13 1099 c 2.488536 m 0.000000 -14.500000 -8.547619 279160.000000 14 1100 m 1.404336 f 0.000000 9.500000 -0.547619 -77570.000000 15 1114 m -0.312264 f 0.000000 -10.500000 -12.547619 141560.000000 16 1119 m -1.374564 m 0.000000 -7.500000 18.452381 110660.000000 17 1123 m 0.988136 m 0.000000 33.500000 16.452381 -27400.000000 18 1125 c 0.287236 f 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 c -1.820864 m 0.000000 -14.500000 -12.547619 348770.000000 20 1128 c -1.338964 f 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 c -2.086464 f 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 m 1.324936 m 0.000000 12.500000 23.452381 -108080.000000 23 1139 m 0.875936 f 0.000000 -4.500000 0.452381 -199980.000000 24 1142 m -0.851664 f 0.000000 10.500000 2.452381 -386850.000000 25 1143 m -2.820164 f 0.000000 11.500000 -13.547619 -109600.000000 26 1153 m -2.458764 f 0.000000 13.500000 10.452381 369170.000000 27 1154 m -1.234964 f 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 c 1.034736 f 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 m 1.163436 f 0.000000 11.500000 11.452381 -71900.000000 30 1163 m 1.371436 m 0.000000 15.500000 7.452381 239550.000000 31 1165 m -0.517664 m 1.000000 -11.500000 -2.547619 16810.000000 32 1166 m -2.302764 m 1.000000 -7.500000 1.452381 220140.000000 33 1167 m 0.292736 f 1.000000 12.500000 11.452381 -117810.000000 34 1171 c 1.385136 f 0.000000 6.500000 -7.547619 59040.000000 35 1173 c 1.075736 f 0.000000 -7.500000 2.452381 -86380.000000 36 1175 c 1.765736 f 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 c 1.732836 m 0.000000 -11.500000 -3.547619 108560.000000 38 1177 m 0.717136 f 0.000000 -5.500000 10.452381 -53070.000000 39 1178 m -0.241164 f 0.000000 33.500000 15.452381 -110020.000000 40 1179 c 0.944336 f 0.000000 -7.500000 0.452381 15300.000000 41 1180 c 0.760936 f 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 c -0.380764 f 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment discrete 2 1 c 2 m 2 age_demean continuous 0 3 sex discrete 2 1 m 2 f 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age_demean -0.000 1.410 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248
Number of subjects: 42 Number of factors: 7 (2 discrete, 5 continuous) Number of classes: 4 Number of regressors: 24 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [Katie.McLaughlin@childrens.harvard.edu] Sent: Friday, August 01, 2014 5:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] GLM error in QDEC
Hi Doug,
Same error when data table created in Linux
There are a number of messages about this same issue in the Archive (e.g.):
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033471...
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.ht...
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036226....
In the second message string, there is some information about bash vs sh in ubuntu potentially generating this error. However, I'm working on a cluster used by a number of others and can't use the fix described by another FS user.
I'm wondering if you've resolved this using another strategy previously?
Thanks, Kate
Error Output:
Reading /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/tktools/tkUtils.tcl
Using /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/lib/tcl/fsgdfPlot.tcl
Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42
Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR Too many subjects not found! Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 0.763636 m 0.000000 1.500000 -3.547619 348130.000000 2 1014 c 0.098336 m 0.000000 -11.500000 -10.547619 149370.000000 3 1032 c 2.507636 m 0.000000 2.500000 0.452381 -960.000000 4 1034 c 0.101136 m 0.000000 -15.500000 -11.547619 190570.000000 5 1041 m -2.516264 m 1.000000 17.500000 12.452381 -26620.000000 6 1043 m -1.453964 m 0.000000 7.500000 12.452381 205250.000000 7 1047 c -0.933764 m 0.000000 -10.500000 -0.547619 -73620.000000 8 1058 m 1.171636 f 0.000000 14.500000 7.452381 -42730.000000 9 1077 c 0.281836 f 0.000000 -16.500000 -12.547619 -40610.000000 10 1094 m 0.142136 f 0.000000 3.500000 -1.547619 -158930.000000 11 1096 c -1.711364 f 0.000000 -6.500000 -6.547619 31690.000000 12 1097 c -0.323264 f 0.000000 6.500000 0.452381 -218300.000000 13 1099 c 2.488536 m 0.000000 -14.500000 -8.547619 279160.000000 14 1100 m 1.404336 f 0.000000 9.500000 -0.547619 -77570.000000 15 1114 m -0.312264 f 0.000000 -10.500000 -12.547619 141560.000000 16 1119 m -1.374564 m 0.000000 -7.500000 18.452381 110660.000000 17 1123 m 0.988136 m 0.000000 33.500000 16.452381 -27400.000000 18 1125 c 0.287236 f 0.000000 -7.500000 -8.547619 -67320.000000 19 1126 c -1.820864 m 0.000000 -14.500000 -12.547619 348770.000000 20 1128 c -1.338964 f 0.000000 -0.500000 -6.547619 -101590.000000 21 1134 c -2.086464 f 0.000000 -4.500000 -5.547619 -42360.000000 22 1137 m 1.324936 m 0.000000 12.500000 23.452381 -108080.000000 23 1139 m 0.875936 f 0.000000 -4.500000 0.452381 -199980.000000 24 1142 m -0.851664 f 0.000000 10.500000 2.452381 -386850.000000 25 1143 m -2.820164 f 0.000000 11.500000 -13.547619 -109600.000000 26 1153 m -2.458764 f 0.000000 13.500000 10.452381 369170.000000 27 1154 m -1.234964 f 0.000000 -8.500000 -2.547619 -261410.000000 28 1157 c 1.034736 f 1.000000 -10.500000 -6.547619 -67330.000000 29 1158 m 1.163436 f 0.000000 11.500000 11.452381 -71900.000000 30 1163 m 1.371436 m 0.000000 15.500000 7.452381 239550.000000 31 1165 m -0.517664 m 1.000000 -11.500000 -2.547619 16810.000000 32 1166 m -2.302764 m 1.000000 -7.500000 1.452381 220140.000000 33 1167 m 0.292736 f 1.000000 12.500000 11.452381 -117810.000000 34 1171 c 1.385136 f 0.000000 6.500000 -7.547619 59040.000000 35 1173 c 1.075736 f 0.000000 -7.500000 2.452381 -86380.000000 36 1175 c 1.765736 f 0.000000 -1.500000 -6.547619 -31300.000000 37 1176 c 1.732836 m 0.000000 -11.500000 -3.547619 108560.000000 38 1177 m 0.717136 f 0.000000 -5.500000 10.452381 -53070.000000 39 1178 m -0.241164 f 0.000000 33.500000 15.452381 -110020.000000 40 1179 c 0.944336 f 0.000000 -7.500000 0.452381 15300.000000 41 1180 c 0.760936 f 0.000000 -18.500000 -13.547619 -97800.000000 42 1181 c -0.380764 f 0.000000 -9.500000 -7.547619 -60610.000000 1 maltreatment discrete 2 1 c 2 m 2 age_demean continuous 0 3 sex discrete 2 1 m 2 f 4 hs_less continuous 0 5 internal_demean continuous 0 6 external_demean continuous 0 7 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age_demean -0.000 1.410 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV_demean 4609.048 168177.248
Number of subjects: 42 Number of factors: 7 (2 discrete, 5 continuous) Number of classes: 4 Number of regressors: 24 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3'
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 5:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC
How did you create your qdec table? It looks like it might have been created on a windows machine. If so, try creating it in linux. doug
On 08/01/2014 04:53 PM, McLaughlin, Katie wrote:
Hi Doug,
The issue seems to be that qdec can't find the subjects in the SUBJECTS_DIR (see output below) when loading the data table.
The subjects are all in the directory, however, with permissions set to 777 on all. I've found a number of previous posts with the same error, but no solution.
Thanks, Kate
Output from loading data table: Loading data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 8 fsid column: 1 Number of factors: 7 Number of subjects: 42
Data table /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1009' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1014' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1032' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1034' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1041' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1043' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1047' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1058' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1077' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1094' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1096' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1097' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1099' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1100' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1114' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1119' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1123' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1125' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1126' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1128' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1134' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1137' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1139' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1142' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1143' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1153' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1154' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1165' in SUBJECTS_DIR Too many subjects not found! Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 4:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC
So, did it generate the error when you loaded the table or when you hit analyze? List the steps and buttons that produce this error. doug
On 07/31/2014 05:20 PM, McLaughlin, Katie wrote:
Hi Doug,
I'm using 5.3.
This error was generated when I had more variables in the model, so I used the option within qdec to remove variables from the data table to see if that had any effect (i.e., deleted everything except one categorical variable). Still got the error you see below.
Thanks, Kate
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, July 31, 2014 5:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC
What version of FS are you using? When I load that file in 5.3 qdec, it creates several discrete classes, see below doug
40 1179 c 17.514000 0.944336 f 12.000000 14.000000 0.000000-7.500000 0.452381 1565300.000000 15300.000000 41 1180 c 17.330600 0.760936 f 1.000000 0.000000 0.000000 -18.500000 -13.547619 1452200.000000 -97800.000000 42 1181 c 16.188900 -0.380764 f 10.000000 6.000000 0.000000 -9.500000 -7.547619 1489390.000000 -60610.000000 1 maltreatment discrete 2 1 c 2 m 2 age continuous 0 3 age_demean continuous 0 4 sex discrete 2 1 m 2 f 5 internalizing continuous 0 6 externalizing continuous 0 7 hs_less continuous 0 8 internal_demean continuous 0 9 external_demean continuous 0 10 ICV continuous 0 11 ICV_demean continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 16.570 1.410 age_demean -0.000 1.410 internalizing 19.500 12.769 externalizing 13.548 9.759 hs_less 0.119 0.328 internal_demean 0.000 12.769 external_demean 0.000 9.759 ICV 1554609.048 168177.248 ICV_demean 4609.048 168177.248
Number of subjects: 42 Number of factors: 11 (2 discrete, 9 continuous) Number of classes: 4 Number of regressors: 40
On 07/31/2014 02:27 PM, McLaughlin, Katie wrote:
Hi Doug et al,
I'm trying to run an analysis in QDEC and continue to get an error that says that the QDEC GLM design creates 0 factors.
I'm attaching my data table here as well as the output of QDEC. I've tried deleting all variables in my data file other than one and testing just that comparison, but no luck.
Any thoughts are much appreciated.
Thanks, Kate
SUBJECTS_DIR is '/net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/SAS/FreeSurfer/FS_5.3' Input table: /neuro/labs/sheridanlab/projects/SAS/FreeSurfer/FS_5.3/qdec/qdec.table.maltreatment.dat Subj#, SubjID, Data... 1 1009 c 2 1014 c 3 1032 c 4 1034 c 5 1041 m 6 1043 m 7 1047 c 8 1058 m 9 1077 c 10 1094 m 11 1096 c 12 1097 c 13 1099 c 14 1100 m 15 1114 m 16 1119 m 17 1123 m 18 1125 c 19 1126 c 20 1128 c 21 1134 c 22 1137 m 23 1139 m 24 1142 m 25 1143 m 26 1153 m 27 1154 m 28 1157 c 29 1158 m 30 1163 m 31 1165 m 32 1166 m 33 1167 m 34 1171 c 35 1173 c 36 1175 c 37 1176 c 38 1177 m 39 1178 m 40 1179 c 41 1180 c 42 1181 c 1 maltreatment discrete 2 1 c 2 m Continuous Factors: Mean: StdDev: ------------------- ----- -------
Number of subjects: 42 Number of factors: 1 (1 discrete, 0 continuous) Number of classes: 2 Number of regressors: 2 ============================================================ ERROR: QdecGlmDesign::Create: zero factors!
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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