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-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 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 12.000000 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! >>> >>> >>> >>> _______________________________________________ >>> 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. >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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
