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-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@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-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: 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-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: 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
>
> _______________________________________________
> 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
>
>
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