[Freesurfer] WM Edits not updating in batch

[McLaughlin, Katie]

Hello Freesurfer Experts,

I'm trying to troubleshoot a problem where the main surface in our brains is 
not adjusting following white matter edits using Freesurfer 5.3. To be clear, 
the procedure here is:

1) Make edits to wm.mgz
2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3

Following this process, what we see is that the main surface in the brain still 
encompasses areas that were deleted from wm.mgz. Here is an example (at bottom 
of the inferior temporal lobe):
[Inline image 1]


This seems to be true for all the edits we've made on this set of brains.

There are no errors in recon-all.log, and the right brain is being recon'd. 
Files in the surf directory seem to be updated as expected. Any idea what we're 
missing here? We haven't had trouble with this process in the past. Any help 
would be much appreciated!

Thanks,
Kate

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[Freesurfer] Research Coordinator Position at the University of Washington

[McLaughlin, Katie]

An experienced, independent, and organized individual is sought for a full-time 
Research Study Coordinator position in the Stress and Development Laboratory at 
the University of Washington Psychology Department, run by Katie McLaughlin, 
PhD.  The individual in this position would coordinate the operations of a 
child clinical psychology laboratory focused on studying the impact of trauma 
exposure on children’s brain and behavioral development.  Principle 
responsibilities include developing, coordinating, and monitoring research 
activities for several psychophysiology and neuroimaging studies of children 
and adolescents; recruiting children, adolescents, and parents from community 
sources; conducting clinical interviews and neuropsychological tests; 
supervising and monitoring undergraduate research assistants; and coordinating 
the management of study data. This position would be an excellent fit for 
applicants interested in obtaining doctoral training in clinical or 
developmental psychology or developmental cognitive neuroscience.

Specific duties include:
·Assistance in the development of recruitment methods; recruitment and 
screening of
 potential participants to determine eligibility.
·Assistance in the preparation of IRB applications, consent forms and 
progress reports
 for institutional review board.
·Development and implementation of standardized protocols for 
collecting and scoring
 behavioral, psychophysiology, and fMRI data.
·Data collection and data quality control to ensure fidelity to study 
protocol
·Development and programming of behavioral and fMRI tasks
.Recruitment, training and supervision of volunteer undergraduate and 
post-
 baccalaureate research assistants.
.Administration of neuropsychological tests and clinical interviews

Previous research or clinical experience with children and the ability to work 
in command line environments such as Unix or Linux operating systems is 
preferred.

The position begins in August or September 2013.  Please email a CV and cover 
letter to Katie McLaughlin at: mclau...@uw.edu.

--
Katie McLaughlin, Ph.D.
Director, Stress & Development Laboratory, Boston Children's Hospital
Assistant Professor of Pediatrics and Psychiatry
Harvard Medical School
21 Autumn Street, Boston, MA 02115
Phone: (857) 218-5598; Fax: (617) 730-0957
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[Freesurfer] GLM error in QDEC

[McLaughlin, Katie]

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!



qdec.table.maltreatment.dat
Description: qdec.table.maltreatment.dat
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Re: [Freesurfer] GLM error in QDEC

[McLaughlin, Katie]

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
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--
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/

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Re: [Freesurfer] GLM error in QDEC

[McLaughlin, Katie]

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!
>
>
>
> __

Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

[McLaughlin, Katie]

Hi Andre and Bruce,

Thanks for your input here.  The sat band has helped, although it hasn't 
entirely corrected the problem (the image attached was from a subject with the 
sat bands included).  We are using a local transmit coil.

I'm going to check with our physicist about the inversion pulse - thanks for 
the suggestion.  

Any other thoughts about strategies for improving this are welcome!  Andre, 
would you mind sharing how you segmented the blood vessels and labeled in 
FreeSurfer? We could try that approach...

Thanks,
Kate


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Andre van der Kouwe 
[an...@nmr.mgh.harvard.edu]
Sent: Friday, August 01, 2014 1:00 PM
To: Bruce Fischl; Freesurfer support list
Cc: Dylan Tisdall
Subject: Re: [Freesurfer] High intensity blood vessels in children with meMPRAGE

Hi,

Thanks, yes, we have this problem on our scans from the Allegra and 7 T
scanners, where there's a local transmit coil (no body transmit coil)
and therefore blood with non-inverted spins enters the head after the
inversion pulse and appears bright in the images. With our Allegra scans
this has indeed caused problems with FreeSurfer, where the vessels are
included as part of some labelled structures. I did try to segment and
label the vessels with only partial success (since the images are
already collected). In your case, a sat band might help... is your
inversion pulse non-selective? If you have an axial slab and axial
slab-selective inversion, maybe just making the inversion pulse
non-selective will help. If the coil has no coverage of the neck, I
guess your sat band won't work and you'll have to address the issue in
post-processing. Sorry, I don't have a specific solution, but we've also
seen the problem. First thing perhaps is to verify whether you're using
a local transmit coil.

Cheers,

Andre.

On 08/01/2014 12:50 PM, Bruce Fischl wrote:
> Hi Kate
>
> I'll cc Andre and Dylan, but I would have thought some sat bands in the
> neck would do it. I think vessels are usually bright in the mprage, but
> don't usually case problems. Comments welcome....
>
> cheers
>
> Bruce
>
> On Fri, 1 Aug 2014, McLaughlin, Katie wrote:
>
>>
>> Hi Doug, Bruce, et al.
>> We've used the MGH meMPRAGE protocol successfully with children and
>> adolescents previously on a Siemens 3T.  I've recently moved to a new
>> institution and am using the protocol on a Philips 3T Achieva scanner and
>> we've been having a lot of issues with high-intensity blood vessels
>> (appearing bright white and interfering with segmentation in FreeSurfer).
>>  Screenshot of an example attached.
>>
>> We have added some rest slabs/sat bands to the protocol to address
>> this, but
>> it hasn't fully solved the problem.
>>
>> I'm wondering if you have any recommendations about adjusting things in
>> FreeSurfer to help us get better segmentation?
>>
>> Thanks for your thoughts on this,
>> Kate
>>
>>
>>
>>
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Re: [Freesurfer] GLM error in QDEC

[McLaughlin, Katie]

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


_____

Re: [Freesurfer] GLM error in QDEC

[McLaughlin, Katie]

ySubjects: 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 0.00 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 be

Re: [Freesurfer] error loading subjects in QDEC

[McLaughlin, Katie]

x27;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 0.00 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  4609.048    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/

[Freesurfer] QdecGlmDesign::Create: zero factors!

[McLaughlin, Katie]

Hi Doug et al,

After solving one issue with QDEC we have run into another.  I previously 
posted an error related to QDEC being unable to find subjects in the subjects 
directory.  That problem was solved by updating the /bin/sh location for ubuntu 
(will post the solution that worked for us to the archive).

The data table now loads fine, it finds all the discrete and continuous 
factors.  However, I am still getting the following error about the GLM Design 
creating zero factors.  See below.

I can't find any info about this error in the archive.

Any thoughts are much appreciated!

Data table attached.

Thanks,
Kate


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 0.00 0.763636 0.00 0.00 1.50 -3.547619 348130.00
2 1014 0.00 0.098336 0.00 0.00 -11.50 -10.547619 
149370.00
3 1032 0.00 2.507636 0.00 0.00 2.50 0.452381 -960.00
4 1034 0.00 0.101136 0.00 0.00 -15.50 -11.547619 
190570.00
5 1041 1.00 -2.516264 0.00 1.00 17.50 12.452381 
-26620.00
6 1043 1.00 -1.453964 0.00 0.00 7.50 12.452381 205250.00
7 1047 0.00 -0.933764 0.00 0.00 -10.50 -0.547619 
-73620.00
8 1058 1.00 1.171636 1.00 0.00 14.50 7.452381 -42730.00
9 1077 0.00 0.281836 1.00 0.00 -16.50 -12.547619 
-40610.00
   10 1094 1.00 0.142136 1.00 0.00 3.50 -1.547619 -158930.00
   11 1096 0.00 -1.711364 1.00 0.00 -6.50 -6.547619 31690.00
   12 1097 0.00 -0.323264 1.00 0.00 6.50 0.452381 -218300.00
   13 1099 0.00 2.488536 0.00 0.00 -14.50 -8.547619 
279160.00
   14 1100 1.00 1.404336 1.00 0.00 9.50 -0.547619 -77570.00
   15 1114 1.00 -0.312264 1.00 0.00 -10.50 -12.547619 
141560.00
   16 1119 1.00 -1.374564 0.00 0.00 -7.50 18.452381 
110660.00
   17 1123 1.00 0.988136 0.00 0.00 33.50 16.452381 -27400.00
   18 1125 0.00 0.287236 1.00 0.00 -7.50 -8.547619 -67320.00
   19 1126 0.00 -1.820864 0.00 0.00 -14.50 -12.547619 
348770.00
   20 1128 0.00 -1.338964 1.00 0.00 -0.50 -6.547619 
-101590.00
   21 1134 0.00 -2.086464 1.00 0.00 -4.50 -5.547619 
-42360.00
   22 1137 1.00 1.324936 0.00 0.00 12.50 23.452381 
-108080.00
   23 1139 1.00 0.875936 1.00 0.00 -4.50 0.452381 -199980.00
   24 1142 1.00 -0.851664 1.00 0.00 10.50 2.452381 
-386850.00
   25 1143 1.00 -2.820164 1.00 0.00 11.50 -13.547619 
-109600.00
   26 1153 1.00 -2.458764 1.00 0.00 13.50 10.452381 
369170.00
   27 1154 1.00 -1.234964 1.00 0.00 -8.50 -2.547619 
-261410.00
   28 1157 0.00 1.034736 1.00 1.00 -10.50 -6.547619 
-67330.00
   29 1158 1.00 1.163436 1.00 0.00 11.50 11.452381 -71900.00
   30 1163 1.00 1.371436 0.00 0.00 15.50 7.452381 239550.00
   31 1165 1.00 -0.517664 0.00 1.00 -11.50 -2.547619 
16810.00
   32 1166 1.00 -2.302764 0.00 1.00 -7.50 1.452381 220140.00
   33 1167 1.00 0.292736 1.00 1.00 12.50 11.452381 
-117810.00
   34 1171 0.00 1.385136 1.00 0.00 6.50 -7.547619 59040.00
   35 1173 0.00 1.075736 1.00 0.00 -7.50 2.452381 -86380.00
   36 1175 0.00 1.765736 1.00 0.00 -1.50 -6.547619 -31300.00
   37 1176 0.00 1.732836 0.00 0.00 -11.50 -3.547619 
108560.00
   38 1177 1.00 0.717136 1.00 0.00 -5.50 10.452381 -53070.00
   39 1178 1.00 -0.241164 1.00 0.00 33.50 15.452381 
-110020.00
   40 1179 0.00 0.944336 1.00 0.00 -7.50 0.452381 15300.00
   41 1180 0.00 0.760936 1.00 0.00 -18.50 -13.547619 
-97800.00
   42 1181 0.00 -0.380764 1.00 0.00 -9.50 -7.547619 
-60610.00
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

Re: [Freesurfer] GLM error in QDEC - SOLUTION

[McLaughlin, Katie]

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 

Re: [Freesurfer] error loading subjects in QDEC

[McLaughlin, Katie]

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 0.00012.769
external_demean 0.000 9.759
 ICV_demean  4609.048168177.248

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 +, 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: QdecProje

Re: [Freesurfer] error loading subjects in QDEC

[McLaughlin, Katie]

Hi Nick,

We solved this.

Thanks for your help,
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: Monday, August 11, 2014 3:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] error loading subjects in QDEC

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 0.00 0.763636 0.00 0.00 1.50 -3.547619 348130.00
2 1014 0.00 0.098336 0.00 0.00 -11.50 -10.547619 
149370.00
3 1032 0.00 2.507636 0.00 0.00 2.50 0.452381 -960.00
4 1034 0.00 0.101136 0.00 0.00 -15.50 -11.547619 
190570.00
5 1041 1.00 -2.516264 0.00 1.00 17.50 12.452381 
-26620.00
6 1043 1.00 -1.453964 0.00 0.00 7.50 12.452381 205250.00
7 1047 0.00 -0.933764 0.00 0.00 -10.50 -0.547619 
-73620.00
8 1058 1.00 1.171636 1.00 0.00 14.50 7.452381 -42730.00
9 1077 0.00 0.281836 1.00 0.00 -16.50 -12.547619 
-40610.00
   10 1094 1.00 0.142136 1.00 0.00 3.50 -1.547619 -158930.00
   11 1096 0.00 -1.711364 1.00 0.00 -6.50 -6.547619 31690.00
   12 1097 0.00 -0.323264 1.00 0.00 6.50 0.452381 -218300.00
   13 1099 0.00 2.488536 0.00 0.00 -14.50 -8.547619 
279160.00
   14 1100 1.00 1.404336 1.00 0.00 9.50 -0.547619 -77570.00
   15 1114 1.00 -0.312264 1.00 0.00 -10.50 -12.547619 
141560.00
   16 1119 1.00 -1.374564 0.00 0.00 -7.50 18.452381 
110660.00
   17 1123 1.00 0.988136 0.00 0.00 33.50 16.452381 -27400.00
   18 1125 0.00 0.287236 1.00 0.00 -7.50 -8.547619 -67320.00
   19 1126 0.00 -1.820864 0.00 0.00 -14.50 -12.547619 
348770.00
   20 1128 0.00 -1.338964 1.00 0.00 -0.50 -6.547619 
-101590.00
   21 1134 0.00 -2.086464 1.00 0.00 -4.50 -5.547619 
-42360.00
   22 1137 1.00 1.324936 0.00 0.00 12.50 23.452381 
-108080.00
   23 1139 1.00 0.875936 1.00 0.00 -4.50 0.452381 -199980.00
   24 1142 1.00 -0.851664 1.00 0.00 10.50 2.452381 
-386850.00
   25 1143 1.00 -2.820164 1.00 0.00 11.50 -13.547619 
-109600.00
   26 1153 1.00 -2.458764 1.00 0.00 13.50 10.452381 
369170.00
   27 1154 1.00 -1.234964 1.00 0.00 -8.50 -2.547619 
-261410.00
   28 1157 0.00 1.034736 1.00 1.00 -10.50 -6.547619 
-67330.00
   29 1158 1.00 1.163436 1.00 0.00 11.50 11.452381 -71900.00
   30 1163 1.00 1.371436 0.00 0.00 15.50 7.452381 239550.00
   31 1165 1.00 -0.517664 0.00 1.00 -11.50 -2.547619 
16810.00
   32 1166 1.00 -2.302764 0.00 1.00 -7.50 1.452381 220140.00
   33 1167 1.00 0.292736 1.00 1.00 12.50 11.452381 
-117810.00
   34 1171 0.00 1.385136 1.00 0.00 6.50 -7.547619 59040.00
   35 1173 0.00 1.075736 1.00 0.00 -7.50 2.452381 -86380.00
   36 1175 0.00 1.765736 1.00 0.00 -1.50 -6.547619 -31300.00
   37 1176 0.00 1.732836 0.00 0.00 -11.50 -3.547619 
108560.00
   38 1177 1.00 0.717136 1.00 0.00 -5.50 10.452381 -53070.00
   39 1178 1.00 -0.241164 1.

[Freesurfer] Research Assistant Position at the University of Washington

[McLaughlin, Katie]

Research Assistant Position
Integrated Brain Imaging Center
University of Washington

An experienced, independent, and organized individual is sought for a full-time 
Research Coordinator position working with Natalia Kleinhans, Ph.D., and Katie 
McLaughlin, Ph.D., at the Integrated Brain Imaging Center at the University of 
Washington.  The individual in this position would assist with data collection 
and data processing for two neuroimaging studies of children.

Principal duties include: 1) assisting with the administration and support of 
research projects and activities, including participant recruitment, 
development of surveys and flyers, and programming fMRI tasks; 2) assisting in 
data collection through active interaction with child participants, including 
telephone screening interviews, in-person interviews, and fMRI data 
acquisition; and 3) conducting pre-processing and analysis of MRI, fMRI, DTI, 
and MRS data. Ability to work in command line operating systems (Linux) and 
perform basic shell scripting is required. Previous research or clinical 
experience with children and experience with other programming languages (e.g., 
python) is preferred.

This position would be an excellent fit for applicants interested in obtaining 
doctoral training in cognitive neuroscience, clinical psychology, or 
developmental psychology.




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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] Research Assistant Position at the University of Washington

[McLaughlin, Katie]

Research Assistant Position
Integrated Brain Imaging Center
University of Washington

An experienced, independent, and organized individual is sought for a full-time 
Research Coordinator position working with Natalia Kleinhans, Ph.D., and Katie 
McLaughlin, Ph.D., at the Integrated Brain Imaging Center at the University of 
Washington.  The individual in this position would assist with data collection 
and data processing for two neuroimaging studies of children.

Principal duties include: 1) assisting with the administration and support of 
research projects and activities, including participant recruitment, 
development of surveys and flyers, and programming fMRI tasks; 2) assisting in 
data collection through active interaction with child participants, including 
telephone screening interviews, in-person interviews, and fMRI data 
acquisition; and 3) conducting pre-processing and analysis of MRI, fMRI, DTI, 
and MRS data. Ability to work in command line operating systems (Linux) and 
perform basic shell scripting is required. Previous research or clinical 
experience with children and experience with other programming languages (e.g., 
python) is preferred.

This position would be an excellent fit for applicants interested in obtaining 
doctoral training in cognitive neuroscience, clinical psychology, or 
developmental psychology.

To find more information and apply, go to the following website: 
https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szLocationID=88
Enter req # 111826
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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.