Re: [Freesurfer] GLM error in QDEC - SOLUTION
Solution to the issue with QDEC being unable to find subjects in the subjects directory with the following fix: sudo mv /bin/sh /bin/sh.orig sudo ln -s /bin/bash /bin/sh Thanks, Kate From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [katie.mclaugh...@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.html https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-October/008618.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036226.html 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
Re: [Freesurfer] GLM error in QDEC
Hi Doug, Just wanted to follow up on this. I'm getting the error that says that the QDEC GLM design creates 0 factors, regardless of how many of the factors in the data table I sent are included in the design. (There are a total of 2 discrete and 9 continuous variables in the data table.) I haven't been able to find any information on this error in the archive - would love your thoughts. Thanks, Kate From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [katie.mclaugh...@childrens.harvard.edu] Sent: Thursday, July 31, 2014 5:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] GLM error in QDEC 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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 12.00 14.00 0.00 -7.50 0.452381 1565300.00 15300.00 41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00 -18.50 -13.547619 1452200.00 -97800.00 42 1181 c 16.188900 -0.380764 f 10.00 6.00 0.00 -9.50 -7.547619 1489390.00 -60610.00 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: --- - --- age16.570 1.410 age_demean-0.000 1.410 internalizing19.50012.769 externalizing13.548 9.759 hs_less 0.119 0.328 internal_demean 0.00012.769 external_demean 0.000 9.759 ICV 1554609.048168177.248 ICV_demean 4609.048168177.248 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! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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 12.00 14.00 0.00 -7.50 0.452381 1565300.00 15300.00 41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00 -18.50 -13.547619 1452200.00 -97800.00 42 1181 c 16.188900 -0.380764 f 10.00 6.00 0.00 -9.50 -7.547619 1489390.00 -60610.00 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: --- - --- age16.570 1.410 age_demean-0.000 1.410 internalizing19.50012.769 externalizing13.548 9.759 hs_less 0.119 0.328 internal_demean 0.00012.769 external_demean 0.000 9.759 ICV 1554609.048168177.248 ICV_demean 4609.048168177.248 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! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed
Re: [Freesurfer] GLM error in QDEC
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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
Re: [Freesurfer] GLM error in QDEC
[gr...@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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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 12.00 14.00 0.00 -7.50 0.452381 1565300.00 15300.00 41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00 -18.50 -13.547619 1452200.00 -97800.00 42 1181 c 16.188900 -0.380764 f 10.00 6.00 0.00 -9.50 -7.547619 1489390.00 -60610.00 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: --- - --- age16.570 1.410 age_demean-0.000 1.410 internalizing19.50012.769 externalizing13.548 9.759 hs_less 0.119 0.328 internal_demean 0.00012.769 external_demean 0.000 9.759 ICV 1554609.048168177.248 ICV_demean 4609.048168177.248 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! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] GLM error in QDEC
... 1 1009 c 0.763636 m 0.00 1.50 -3.547619 348130.00 2 1014 c 0.098336 m 0.00 -11.50 -10.547619 149370.00 3 1032 c 2.507636 m 0.00 2.50 0.452381 -960.00 4 1034 c 0.101136 m 0.00 -15.50 -11.547619 190570.00 5 1041 m -2.516264 m 1.00 17.50 12.452381 -26620.00 6 1043 m -1.453964 m 0.00 7.50 12.452381 205250.00 7 1047 c -0.933764 m 0.00 -10.50 -0.547619 -73620.00 8 1058 m 1.171636 f 0.00 14.50 7.452381 -42730.00 9 1077 c 0.281836 f 0.00 -16.50 -12.547619 -40610.00 10 1094 m 0.142136 f 0.00 3.50 -1.547619 -158930.00 11 1096 c -1.711364 f 0.00 -6.50 -6.547619 31690.00 12 1097 c -0.323264 f 0.00 6.50 0.452381 -218300.00 13 1099 c 2.488536 m 0.00 -14.50 -8.547619 279160.00 14 1100 m 1.404336 f 0.00 9.50 -0.547619 -77570.00 15 1114 m -0.312264 f 0.00 -10.50 -12.547619 141560.00 16 1119 m -1.374564 m 0.00 -7.50 18.452381 110660.00 17 1123 m 0.988136 m 0.00 33.50 16.452381 -27400.00 18 1125 c 0.287236 f 0.00 -7.50 -8.547619 -67320.00 19 1126 c -1.820864 m 0.00 -14.50 -12.547619 348770.00 20 1128 c -1.338964 f 0.00 -0.50 -6.547619 -101590.00 21 1134 c -2.086464 f 0.00 -4.50 -5.547619 -42360.00 22 1137 m 1.324936 m 0.00 12.50 23.452381 -108080.00 23 1139 m 0.875936 f 0.00 -4.50 0.452381 -199980.00 24 1142 m -0.851664 f 0.00 10.50 2.452381 -386850.00 25 1143 m -2.820164 f 0.00 11.50 -13.547619 -109600.00 26 1153 m -2.458764 f 0.00 13.50 10.452381 369170.00 27 1154 m -1.234964 f 0.00 -8.50 -2.547619 -261410.00 28 1157 c 1.034736 f 1.00 -10.50 -6.547619 -67330.00 29 1158 m 1.163436 f 0.00 11.50 11.452381 -71900.00 30 1163 m 1.371436 m 0.00 15.50 7.452381 239550.00 31 1165 m -0.517664 m 1.00 -11.50 -2.547619 16810.00 32 1166 m -2.302764 m 1.00 -7.50 1.452381 220140.00 33 1167 m 0.292736 f 1.00 12.50 11.452381 -117810.00 34 1171 c 1.385136 f 0.00 6.50 -7.547619 59040.00 35 1173 c 1.075736 f 0.00 -7.50 2.452381 -86380.00 36 1175 c 1.765736 f 0.00 -1.50 -6.547619 -31300.00 37 1176 c 1.732836 m 0.00 -11.50 -3.547619 108560.00 38 1177 m 0.717136 f 0.00 -5.50 10.452381 -53070.00 39 1178 m -0.241164 f 0.00 33.50 15.452381 -110020.00 40 1179 c 0.944336 f 0.00 -7.50 0.452381 15300.00 41 1180 c 0.760936 f 0.00 -18.50 -13.547619 -97800.00 42 1181 c -0.380764 f 0.00 -9.50 -7.547619 -60610.00 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 0.00012.769 external_demean 0.000 9.759 ICV_demean 4609.048168177.248 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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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
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 12.00 14.00 0.00 -7.50 0.452381 1565300.00 15300.00 41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00 -18.50 -13.547619 1452200.00 -97800.00 42 1181 c 16.188900 -0.380764 f 10.00 6.00 0.00 -9.50 -7.547619 1489390.00 -60610.00 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: --- - --- age16.570 1.410 age_demean-0.000 1.410 internalizing19.50012.769 externalizing13.548 9.759 hs_less 0.119 0.328 internal_demean 0.00012.769 external_demean 0.000 9.759 ICV 1554609.048168177.248 ICV_demean 4609.048168177.248 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! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] GLM error in QDEC
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@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 12.00 14.00 0.00 -7.50 0.452381 1565300.00 15300.00 41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00 -18.50 -13.547619 1452200.00 -97800.00 42 1181 c 16.188900 -0.380764 f 10.00 6.00 0.00 -9.50 -7.547619 1489390.00 -60610.00 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: --- - --- age16.570 1.410 age_demean-0.000 1.410 internalizing19.50012.769 externalizing13.548 9.759 hs_less 0.119 0.328 internal_demean 0.00012.769 external_demean 0.000 9.759 ICV 1554609.048168177.248 ICV_demean 4609.048168177.248 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! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e
