[Freesurfer] Qdec table

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Hi Freesurfer devs,

How can I create a qdec.table.dat file? I tried using a txt file but it
doesn´t works. I attached the qdec.table.dat file that I have created.

Sorry for this absurd question and thanks in advance.

Cheers,

-- 
*Miguel Ángel Rivas Fernández*


qdec.table.dat
Description: Binary data
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[Freesurfer] Qdec+Table format issue ?????

[Dimitrios Trifonopoulos]

Dear Recipient,


I am a Master student new comer in FS. I am trying toi use the QDEC ti analyse 
some longitudinal data. Most probably my issue is related with the file format. 
I tried to use several text editors (mac text editor, gedit and text wrangler) 
however I end up in 2 different errors without be able to overcome the issue.

The 1st error was:


 ERROR: qdec table missing correct column headers?

   Make sure first column is labeled 'fsid' for the time point and

   second column is 'fsid-base' to specify the subject tempate (base), e.g.:


 fsidfsid-base   age

 me1 me  22.3

 me2 me  23.2

 you1you 21.6

 you2you 22.5


Simones-iMac:subjects SLMAC14$ long_mris_slopes --qdec 
/Applications/freesurfer/subjects/qdec/lala copy.dat.doc --meas thickness 
--hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
years --qcache fsaverage --sd /Applications/freesurfer/subjects/


and the 2nd one was:


Parsing the qdec table: /Applications/freesurfer/subjects/qdec/qdec.table.dat

ERROR: qdec table /Applications/freesurfer/subjects/qdec/qdec.table.dat not 
found or empty?


Even if I found a similar error im the forum, I didn't understand finally how 
this guy overcome it. I also attached you the 2 files that I used. Please 
answer me as soon as you are available. Thank you


All the Best,

Dimitris








qdec.table.dat
Description: qdec.table.dat
{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf200
{\fonttbl\f0\fnil\fcharset0 Menlo-Regular;\f1\fswiss\fcharset0 Helvetica;}
{\colortbl;\red255\green255\blue255;}
{\*\expandedcolortbl;;}
\paperw11900\paperh16840\margl1440\margr1440\vieww10800\viewh8400\viewkind0
\deftab720
\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardeftab720\ri380\partightenfactor0

\f0\fs22 \cf0 fsid fsid-base
\f1\fs24  age\
\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\pardeftab720\ri380\partightenfactor0
\cf0 20101DOJ_M0 20101DOJ_template 6420101DOJ_M12 20101DOJ_template 65\
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Re: [Freesurfer] Qdec Table Loading Error

[Douglas N Greve]

there are lots of strange characters in that file (as revealed with the 
od octal dump program). Maybe run dos2unix on the file or create it from 
scratch.


On 12/14/2017 12:00 PM, Arsenije Subotic wrote:
>
> Hi Douglas,
>
>
> I tried doing that but it seems that the issue is that when I open 
> Qdec it does not recognize any of the files in the folder as a data 
> file (.dat).
>
>
> Thanks,
>
> Arsenije
>
> 
> *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> *Sent:* Thursday, December 14, 2017 9:47:54 AM
> *To:* Arsenije Subotic
> *Subject:* Re: [Freesurfer] Qdec Table Loading Error
> The table is not quite the right format. Your first line is
>
>
> lh.aparc.thickness  lh_MeanThickness_thickness
> BrainSegVolNotVent  eTIV    gender  age
>
>
> but it should be
>
>
> fsid lh.aparc.thickness  lh_MeanThickness_thickness
> BrainSegVolNotVent  eTIV    gender  age
>
> try that
>
>
> On 12/12/2017 02:21 PM, Arsenije Subotic wrote:
> >
> > Hi Douglas,
> >
> >
> > Here is the text file I am trying to convert.
> >
> >
> > Thanks,
> >
> > Arsenije
> >
> > --------
> > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> > *Sent:* Tuesday, December 12, 2017 11:52:41 AM
> > *To:* Arsenije Subotic
> > *Subject:* Re: [Freesurfer] Qdec Table Loading Error
> > yes
> >
> >
> >
> > On 12/12/2017 01:48 PM, Arsenije Subotic wrote:
> > > Hi Douglas,
> > >
> > > Is it ok if I can send you the table to your email? I tried
> > uploading my file using the FTP File Exchange but it doesn’t seem to
> > work for me under the put.filename.txt command.
> > >
> > > Thanks,
> > > Arsenije
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
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> > Filedrop is for sending files work-related files up to 2GiB; For files
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> >
> >
> >
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Martinos Center File Drop - nmr.mgh.harvard.edu
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> > 11/15/2012 -- There is a new version of Filedrop. Please help us test
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> > Center file drop area ...
> >
> >
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> >
> >
> >
> > The information in this e-mail is intended only for the person to whom
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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
>
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>

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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[Freesurfer] Qdec Table Loading Error

[Arsenije Subotic]

Dear experts,


I'm currently trying to import some of my data into Qdec in order to perform a 
group analysis on cortical thickness. All of my data was originally in an excel 
sheet and it had the following variables (fsid, gender, age, and thickness). I 
tried converting it into a file that would be opened with Qdec. I use a mac and 
I originally tried to export the file into text editor and I tried saving it as 
"qdec.table.dat", which had no problems being opened in text edit. However, 
when I tried loading it into qdec it gives me an error:"error loading the data 
table". I'm quite new to Qdec (this is my first week trying it). Is there some 
code that I can use to convert my file into a .dat file so that it can be 
compatible with qdec? I tried looking through the previous questions and trying 
some commands (for instance dos2unix -c mac qdec.table.dat, which supposedly 
replaces LF chars with CR chars).


Thanks for your help.


Arsenije
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Re: [Freesurfer] QDEC table .dat

[Douglas Greve]

I don't know what you did, but that is still a binary file not a text file


On 2/7/17 4:27 PM, Leblanc Élizabel wrote:

Hi Freesurfer's expert,

I have some trouble with the dec.table.dat file, as many others as I can see. I 
am using a mac OS x, I took an excel file with my 4 variables and open it in a 
.txt format. then I tried to convert it to a .dat file. I think it worked well 
(I wrote mv qdec.table.txt qdec.table.dat in the command terminal). But when I 
try to load the table using QDEC it still give me this error message.


Loading data table /Applications/freesurfer/subjects/qdec.table.dat...

ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in 
/Applications/freesurfer/subjects/qdec.table.dat!

Error loading the data table.

I have attached to this email my qdec table.

Can you please give me advice on how to create a qdec table (as simple as 
possible because I am not pretty familiar with it to this point).

Thank you very much


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[Freesurfer] QDEC table .dat

[Leblanc Élizabel]

Hi Freesurfer's expert,

I have some trouble with the dec.table.dat file, as many others as I can see. I 
am using a mac OS x, I took an excel file with my 4 variables and open it in a 
.txt format. then I tried to convert it to a .dat file. I think it worked well 
(I wrote mv qdec.table.txt qdec.table.dat in the command terminal). But when I 
try to load the table using QDEC it still give me this error message.


Loading data table /Applications/freesurfer/subjects/qdec.table.dat...

ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in 
/Applications/freesurfer/subjects/qdec.table.dat!

Error loading the data table.

I have attached to this email my qdec table.

Can you please give me advice on how to create a qdec table (as simple as 
possible because I am not pretty familiar with it to this point).

Thank you very much


qdec.table.dat
Description: qdec.table.dat
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Re: [Freesurfer] QDEC table import issue

[Paul Rowley]

It was the spaces! Thanks for the help
On Jan 13, 2017, at 11:40 AM, Douglas N Greve 
> wrote:

I'm not sure that QDEC can read in a CSV file. Can you remove the commas
and try again? You'll also have to remove the spaces between column headings


On 01/13/2017 10:55 AM, Paul Rowley wrote:
Good morning,
I’m experiencing issues importing data into QDEC. When I upload the table, this 
is the error I receive:
Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
Number of columns:  10
fsid column:1
Number of factors:  9
Number of subjects: 19
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: 
L_temporalpole_thickavg for subject NV_002_V1

I’ve attached the table and would greatly appreciate any advice on resolving 
this issue.
Thanks in advance for your help,
Paul


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Re: [Freesurfer] QDEC table import issue

[Douglas N Greve]

I'm not sure that QDEC can read in a CSV file. Can you remove the commas 
and try again? You'll also have to remove the spaces between column headings


On 01/13/2017 10:55 AM, Paul Rowley wrote:
> Good morning,
> I’m experiencing issues importing data into QDEC. When I upload the table, 
> this is the error I receive:
> Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
> Number of columns:  10
> fsid column:1
> Number of factors:  9
> Number of subjects: 19
> ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: 
> L_temporalpole_thickavg for subject NV_002_V1
>
> I’ve attached the table and would greatly appreciate any advice on resolving 
> this issue.
> Thanks in advance for your help,
> Paul
>
>
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-- 
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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
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[Freesurfer] QDEC table import issue

[Paul Rowley]

Good morning,
I’m experiencing issues importing data into QDEC. When I upload the table, this 
is the error I receive: 
Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
Number of columns:  10
fsid column:1
Number of factors:  9
Number of subjects: 19
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: 
L_temporalpole_thickavg for subject NV_002_V1

I’ve attached the table and would greatly appreciate any advice on resolving 
this issue. 
Thanks in advance for your help,
Paul 


qdec.table.dat
Description: qdec.table.dat
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Re: [Freesurfer] qdec table loading error

[Hirsch, Gabriella]

Scratch that - I simply changed the level name from blind to EB and it 
worked. Clearly qdec didn't like my naming assignments.

Thanks anyway!
Gabriella

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella
Sent: Thursday, May 07, 2015 3:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] qdec table loading error

Hi FS experts,

I'm having a really tough time trying to get my qdec.table.dat table to load 
into the qdec GUI. I have gone through the wiki painstakingly and have no idea 
why it's giving me this error message:

Reading /usr/local/freesurfer/tktools/tkUtils.tcl

Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl

Loading data table 
/media/seagate_external_/freesurfer_subjects/qdec/qdec.table.dat...
Number of columns:  2
fsid column:1
Number of factors:  1
Number of subjects: 18
Reading discrete factor levels from config file 
/media/seagate_external_/freesurfer_subjects/qdec/group.levels
control
blind
done.

ERROR: Subject FLY_03072013 has an invalid level 'blind' in the group column
INFO: If 'group' is a discrete factor, then create a file
named 'group.levels' containing the valid factor names
one per line.
Error loading the data table.


For the record, I definitely have a group.levels file in my qdec directory 
with the two levels (blind and control) of the discrete factor (group).

Any ideas?

Thank you!
Gabriella
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[Freesurfer] qdec table loading error

[Hirsch, Gabriella]

Hi FS experts,

I'm having a really tough time trying to get my qdec.table.dat table to load 
into the qdec GUI. I have gone through the wiki painstakingly and have no idea 
why it's giving me this error message:

Reading /usr/local/freesurfer/tktools/tkUtils.tcl

Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl

Loading data table 
/media/seagate_external_/freesurfer_subjects/qdec/qdec.table.dat...
Number of columns:  2
fsid column:1
Number of factors:  1
Number of subjects: 18
Reading discrete factor levels from config file 
/media/seagate_external_/freesurfer_subjects/qdec/group.levels
control
blind
done.

ERROR: Subject FLY_03072013 has an invalid level 'blind' in the group column
INFO: If 'group' is a discrete factor, then create a file
named 'group.levels' containing the valid factor names
one per line.
Error loading the data table.


For the record, I definitely have a group.levels file in my qdec directory 
with the two levels (blind and control) of the discrete factor (group).

Any ideas?

Thank you!
Gabriella
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[Freesurfer] qdec table file

[Laura M. Tully]

Hi Doug,

Attached is the qdec table file and associated levels files. It's strange
that qdec won't let me select more than one continuous variable. What's
even more strange is that I have been able to do that last month when I
originally looked at these data before doing manual edits and quality
control. I don't think that I have changed anything since then, but I'm not
sure what to look for. Any help you have would be most appreciated!

Best,

Laura.

-- 
Laura Tully
Social Neuroscience  Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura




-- 
Laura Tully
Social Neuroscience  Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura


betweenGroup.qdec.table.dat
Description: Binary data


Gender.levels
Description: Binary data


Group.levels
Description: Binary data
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Re: [Freesurfer] qdec table file

[Douglas N Greve]

OK, I've replicated that this is happening, but Nick will have to take a 
look.
doug

On 06/04/2012 11:05 AM, Laura M. Tully wrote:



 Hi Doug,

 Attached is the qdec table file and associated levels files. It's 
 strange that qdec won't let me select more than one continuous 
 variable. What's even more strange is that I have been able to do that 
 last month when I originally looked at these data before doing manual 
 edits and quality control. I don't think that I have changed anything 
 since then, but I'm not sure what to look for. Any help you have would 
 be most appreciated!

 Best,

 Laura.

 -- 
 Laura Tully
 Social Neuroscience  Psychopathology
 Harvard University
 840 William James Hall
 33 Kirkland St
 Cambridge, MA 02138
 ltu...@fas.harvard.edu mailto:ltu...@fas.harvard.edu
 -- 
 My musings as a young clinical scientist: 
 http://theclinicalbrain.blogspot.com/
 Follow me on Twitter: @tully_laura




 -- 
 Laura Tully
 Social Neuroscience  Psychopathology
 Harvard University
 840 William James Hall
 33 Kirkland St
 Cambridge, MA 02138
 ltu...@fas.harvard.edu mailto:ltu...@fas.harvard.edu
 -- 
 My musings as a young clinical scientist: 
 http://theclinicalbrain.blogspot.com/
 Follow me on Twitter: @tully_laura



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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] qdec table

[Laura M. Tully]

Thanks Doug - Nick, do you have any idea what might be happening here? Why
might qdec stop allowing me to select more than one continuous variable?
Thanks!

Laura.


Message: 24
Date: Mon, 04 Jun 2012 11:19:57 -0400
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec table file
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 4fccd21d.4040...@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

OK, I've replicated that this is happening, but Nick will have to take a
look.
doug

On 06/04/2012 11:05 AM, Laura M. Tully wrote:



 Hi Doug,

 Attached is the qdec table file and associated levels files. It's
 strange that qdec won't let me select more than one continuous
 variable. What's even more strange is that I have been able to do that
 last month when I originally looked at these data before doing manual
 edits and quality control. I don't think that I have changed anything
 since then, but I'm not sure what to look for. Any help you have would
 be most appreciated!

 Best,

 Laura.
-- 
Laura Tully
Social Neuroscience  Psychopathology
Harvard University
840 William James Hall
33 Kirkland St
Cambridge, MA 02138
ltu...@fas.harvard.edu
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
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[Freesurfer] QDEC table

[Ignacio Letelier]

Hi freesurfers

Do anyone know if it's possible to automatically enter in the QDEC table the
gray matter volume  of every subject in the study, to avoid
entering this item manually for each one ?

Best regards.
-- 
Ignacio.
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Re: [Freesurfer] QDEC table

[Nick Schmansky]

the 'generate stats data tables' button in the Subjects tab will do
this.  see the section 'Stats Data Import' in the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
which is copied here:


 It is possible to import the aseg and aparc data from the
 FreeSurfer-processed group data. To do so, press the 'Generate Stats
 Data Tables' button. This will run the FreeSurfer utilities
 asegstats2table and aparcstats2table on your group data. Upon
 completion (you should see the progress in the terminal screen), then
 the 'Generate Stats Data Tables' button becomes a menu-selection list.
 Within that menu, you can select 'aseg.volume'. Upon doing so, the
 volumetric data for various subcortical structures are displayed. You
 could choose for example 'Left-Lateral-Ventricle', then click 'Add
 Selection to Data Table'. Upon doing so, it will appear in the
 'Discrete and Continuous Factors' display of the 'Data Table View'.
 'Left-Lateral-Ventricle' is now available as a possible factor in your
 analysis ('Left-Hippocampus' and 'Right-Hippocampus' were imported
 from aseg.volume in this manner). If you select
 'Left-Lateral-Ventricle' in the 'Data Table View', then the volumetric
 data for all the subjects is plotted. You can look for patterns or
 outliers. If you suspect an outlier, right-click on that point in the
 scatter-plot. You can then either exclude that subject, or examine it
 in tkmedit or tksurfer, to check for possible problems in the original
 scan data. Lastly, you can save this newly imported data (in this
 case, 'Left-Lateral-Ventricle') to your qdec.table.dat file by
 selecting 'Save Data Table' from the File menu (but dont do this for
 the tutorial). 
 


n.



On Thu, 2011-07-07 at 09:18 -0400, Ignacio Letelier wrote:
 Hi freesurfers
 
 Do anyone know if it's possible to automatically enter in the QDEC
 table the gray matter volume  of every subject in the study, to avoid 
 entering this item manually for each one ?
 
 Best regards.
 -- 
 Ignacio.
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Re: [Freesurfer] QDEC table loading errors

[Ilana Hairston]

there a line break script, which is somehow installed in my system (Sentos),
which cleans this up.  you basically type lb FILENAME
i can't try and find out what it contains, if you can't get it to work

On 22 September 2010 11:28, James Porter port...@umn.edu wrote:

  Hello-

 I'm having a resurgence of an old problem (
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
 but the old solution is not cutting it. When I try to load a table in QDEC
 1.4, I get the following error:

 Loading data table qdec.table.dat...
 ERROR: QdecDataTable::Load did not find a column named 'fsid', 'ID', or
 'Subject' in the first column of qdec.table.dat!
 Error loading the data table.

 However, the file definitely does have 'fsid' as the first column.

  head qdec.table.dat | awk '{print $1, $2, $3}'
 fsid Sex AgeGrp
 14080 Female Oldr
 14081 Female Oldr
 14286 Female Oldr
 14287 Female Oldr
 14390 Female Oldr
 14391 Male Oldr
 14392 Male Oldr
 14428 Female Oldr
 14430 Male Oldr

 Creating the file on Windows, Mac, and Unix platforms using a variety of
 programs (kate, oocalc, text wrangler, excel, word, notepad, etc) with
 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor does
 running dos2unix on the file(s). Having tab delimited or space delimited
 files doesn't make any difference, either. Trying to open the tables with
 QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change the outcome.

 Any ideas on how to solve this riddle?

 Thanks,
 Jim

 --
 Jim Porter, M.A.
 Graduate Student
 Clinical Science and Psychopathology Research
 University of Minnesota



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 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
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 error
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 properly
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***
Ilana Hairston ,PhD
Research Assistant Professor
4250 Plymouth Rd. (rm 2439)
Psychiatry Department, Addiction Research Center
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Tel: 734-232-0232; Mobile: 650-906-8449
 
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[Freesurfer] QDEC table loading errors

[James Porter]

  
  
Hello-
  
  I'm having a resurgence of an old problem
  (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
  but the old solution is not cutting it. When I try to load a table
  in QDEC 1.4, I get the following error:
  
   Loading data table qdec.table.dat...
   ERROR: QdecDataTable::Load did not find a column named 'fsid',
  'ID', or 'Subject' in the first column of qdec.table.dat!
   Error loading the data table.
  
  However, the file definitely does have 'fsid' as the first column.
  
head qdec.table.dat | awk '{print $1, $2, $3}'
   fsid Sex AgeGrp
   14080 Female Oldr
   14081 Female Oldr
   14286 Female Oldr
   14287 Female Oldr
   14390 Female Oldr
   14391 Male Oldr
   14392 Male Oldr
   14428 Female Oldr
   14430 Male Oldr
  
  Creating the file on Windows, Mac, and Unix platforms using a
  variety of programs (kate, oocalc, text wrangler, excel, word,
  notepad, etc) with 'fsid', 'ID', or 'Subject' as the column title
  doesn't help, nor does running dos2unix on the file(s). Having tab
  delimited or space delimited files doesn't make any difference,
  either. Trying to open the tables with QDEC in Unix (RedHat) or
  Mac (10.6.4) doesn't change the outcome. 
  
  Any ideas on how to solve this riddle?
  
  Thanks,
  Jim

-- 
Jim Porter, M.A.
Graduate Student
Clinical Science and Psychopathology Research
University of Minnesota


  

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Re: [Freesurfer] QDEC table loading errors

[Nick Schmansky]

can you send me the file?  

n.

On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
 Hello-
 
 I'm having a resurgence of an old problem
 (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html) 
 but the old solution is not cutting it. When I try to load a table in QDEC 
 1.4, I get the following error:
 
 Loading data table qdec.table.dat...
 ERROR: QdecDataTable::Load did not find a column named 'fsid',
 'ID', or 'Subject' in the first column of qdec.table.dat!
 Error loading the data table.
 
 However, the file definitely does have 'fsid' as the first column.
 
  head qdec.table.dat | awk '{print $1, $2, $3}'
 fsid Sex AgeGrp
 14080 Female Oldr
 14081 Female Oldr
 14286 Female Oldr
 14287 Female Oldr
 14390 Female Oldr
 14391 Male Oldr
 14392 Male Oldr
 14428 Female Oldr
 14430 Male Oldr
 
 Creating the file on Windows, Mac, and Unix platforms using a variety
 of programs (kate, oocalc, text wrangler, excel, word, notepad, etc)
 with 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor
 does running dos2unix on the file(s). Having tab delimited or space
 delimited files doesn't make any difference, either. Trying to open
 the tables with QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change
 the outcome. 
 
 Any ideas on how to solve this riddle?
 
 Thanks,
 Jim
 -- 
 Jim Porter, M.A.
 Graduate Student
 Clinical Science and Psychopathology Research
 University of Minnesota
 
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Re: [Freesurfer] QDEC table loading errors

[James Porter]

  
  
Of course, once I ask
  for help I stumble immediately upon the solution. There appears to
  be a limit to the number of columns that QDEC is willing to put up
  with when reading in tables. If I create a table that only has the
  few columns that I'm interested in (as opposed to the kitchen sink
  spreadsheet I was working with), then it reads in without
error. 

Thanks for the help by proxy! 
Jim


On 9/22/10 10:38 AM, Nick Schmansky wrote:

  can you send me the file?  

n.

On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:

  
Hello-

I'm having a resurgence of an old problem
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html) but the old solution is not cutting it. When I try to load a table in QDEC 1.4, I get the following error:

Loading data table qdec.table.dat...
ERROR: QdecDataTable::Load did not find a column named 'fsid',
'ID', or 'Subject' in the first column of qdec.table.dat!
Error loading the data table.

However, the file definitely does have 'fsid' as the first column.

 head qdec.table.dat | awk '{print $1, $2, $3}'
fsid Sex AgeGrp
14080 Female Oldr
14081 Female Oldr
14286 Female Oldr
14287 Female Oldr
14390 Female Oldr
14391 Male Oldr
14392 Male Oldr
14428 Female Oldr
14430 Male Oldr

Creating the file on Windows, Mac, and Unix platforms using a variety
of programs (kate, oocalc, text wrangler, excel, word, notepad, etc)
with 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor
does running dos2unix on the file(s). Having tab delimited or space
delimited files doesn't make any difference, either. Trying to open
the tables with QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change
the outcome. 

Any ideas on how to solve this riddle?

Thanks,
Jim
-- 
Jim Porter, M.A.
Graduate Student
Clinical Science and Psychopathology Research
University of Minnesota

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Re: [Freesurfer] QDEC table loading errors

[Nick Schmansky]

there shouldn't be a limit on the number of columns it will read.  the
thing to be careful about is the name of a column.  sometimes when
importing a spreadsheet, a column name will consist of two words (thus
messing-up the detected number of columns), or it will have a minus -
char in the name, which doesnt get interpreted properly.  probably there
is a column name which is not a single word.

n.

On Wed, 2010-09-22 at 10:45 -0500, James Porter wrote:
 Of course, once I ask for help I stumble immediately upon the
 solution. There appears to be a limit to the number of columns that
 QDEC is willing to put up with when reading in tables. If I create a
 table that only has the few columns that I'm interested in (as opposed
 to the kitchen sink spreadsheet I was working with), then it reads in
 without error. 
 
 Thanks for the help by proxy! 
 Jim
 
 
 On 9/22/10 10:38 AM, Nick Schmansky wrote: 
  can you send me the file?  
  
  n.
  
  On Wed, 2010-09-22 at 10:28 -0500, James Porter wrote:
   Hello-
   
   I'm having a resurgence of an old problem
   (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12152.html)
but the old solution is not cutting it. When I try to load a table in 
   QDEC 1.4, I get the following error:
   
   Loading data table qdec.table.dat...
   ERROR: QdecDataTable::Load did not find a column named 'fsid',
   'ID', or 'Subject' in the first column of qdec.table.dat!
   Error loading the data table.
   
   However, the file definitely does have 'fsid' as the first column.
   
head qdec.table.dat | awk '{print $1, $2, $3}'
   fsid Sex AgeGrp
   14080 Female Oldr
   14081 Female Oldr
   14286 Female Oldr
   14287 Female Oldr
   14390 Female Oldr
   14391 Male Oldr
   14392 Male Oldr
   14428 Female Oldr
   14430 Male Oldr
   
   Creating the file on Windows, Mac, and Unix platforms using a variety
   of programs (kate, oocalc, text wrangler, excel, word, notepad, etc)
   with 'fsid', 'ID', or 'Subject' as the column title doesn't help, nor
   does running dos2unix on the file(s). Having tab delimited or space
   delimited files doesn't make any difference, either. Trying to open
   the tables with QDEC in Unix (RedHat) or Mac (10.6.4) doesn't change
   the outcome. 
   
   Any ideas on how to solve this riddle?
   
   Thanks,
   Jim
   -- 
   Jim Porter, M.A.
   Graduate Student
   Clinical Science and Psychopathology Research
   University of Minnesota
   
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[Freesurfer] Qdec table

[Dankner, Nathan (NIH/NIMH) [F]]

Hi all,

I am attempting to create a qdec.table.dat file, and have been unable to find a 
way to paste my data into it in a way that will make it readable.  When I paste 
it in qdec always outputs an error when trying to open it, even if visually the 
file appears to be correct.  Is there an easy way to import data from excel 
into something readable by qdec?  I'm hoping to avoid having to manually enter 
everything because there is quite a lot of data, so any help would be 
appreciated.  Thanks,

Nathan

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Re: [Freesurfer] Qdec table

[Douglas N Greve]

If you're creating the file in windows, try running dos2unix on the file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:
 Hi all,

 I am attempting to create a qdec.table.dat file, and have been unable to find 
 a way to paste my data into it in a way that will make it readable.  When I 
 paste it in qdec always outputs an error when trying to open it, even if 
 visually the file appears to be correct.  Is there an easy way to import data 
 from excel into something readable by qdec?  I'm hoping to avoid having to 
 manually enter everything because there is quite a lot of data, so any help 
 would be appreciated.  Thanks,

 Nathan

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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Qdec table

[Dankner, Nathan (NIH/NIMH) [F]]

Unfortunately I'm not running windows.  Are you familiar with any tricks I can 
use on a mac?


On 11/17/09 5:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

If you're creating the file in windows, try running dos2unix on the file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:
 Hi all,

 I am attempting to create a qdec.table.dat file, and have been unable to find 
 a way to paste my data into it in a way that will make it readable.  When I 
 paste it in qdec always outputs an error when trying to open it, even if 
 visually the file appears to be correct.  Is there an easy way to import data 
 from excel into something readable by qdec?  I'm hoping to avoid having to 
 manually enter everything because there is quite a lot of data, so any help 
 would be appreciated.  Thanks,

 Nathan

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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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Re: [Freesurfer] Qdec table

[Krish Subramaniam]

Some programs notoriously add Ctrl-M at the end of every line ( or  
every cell )

If you have the vi editor you can follow this method 
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/ 
  to remove all the instances of Ctrl-M and again try in qdec.  
Unfortunately I am not able to reproduce the error here because i  
don't have excel.

Here's another method : 
http://www.unix.com/shell-programming-scripting/25658-removing-control-ms-m.html

Best
Krish

On Nov 17, 2009, at 5:21 PM, Dankner, Nathan (NIH/NIMH) [F] wrote:

 Unfortunately I'm not running windows.  Are you familiar with any  
 tricks I can use on a mac?


 On 11/17/09 5:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu  
 wrote:

 If you're creating the file in windows, try running dos2unix on the  
 file.

 doug

 Dankner, Nathan (NIH/NIMH) [F] wrote:
 Hi all,

 I am attempting to create a qdec.table.dat file, and have been  
 unable to find a way to paste my data into it in a way that will  
 make it readable.  When I paste it in qdec always outputs an error  
 when trying to open it, even if visually the file appears to be  
 correct.  Is there an easy way to import data from excel into  
 something readable by qdec?  I'm hoping to avoid having to manually  
 enter everything because there is quite a lot of data, so any help  
 would be appreciated.  Thanks,

 Nathan

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 gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Qdec table

[Derin Cobia]

Nathan,

Here are the steps I use to create QDEC dat files on a Mac:

-Export/save your data in SPSS/Excel as a .csv file
-Open the .csv file in TextWrangler (a free text editor for Mac)
-Do a Find  Replace of the , for spaces  to make it a space  
separated file
-Down at the bottom of the TextWrangler window is a drop down box to  
specify the type of hard returns ('Classic Mac' or 'Unix'); make sure  
the last line ends in a return

-Save as a ~.qdec.table.dat file

Hope that helps.

-Derin


On Nov 17, 2009, at 5:00 PM, Krish Subramaniam wrote:


Some programs notoriously add Ctrl-M at the end of every line ( or
every cell )

If you have the vi editor you can follow this method 
http://www.tech-recipes.com/rx/150/remove-m-characters-at-end-of-lines-in-vi/
 to remove all the instances of Ctrl-M and again try in qdec.
Unfortunately I am not able to reproduce the error here because i
don't have excel.

Here's another method : 
http://www.unix.com/shell-programming-scripting/25658-removing-control-ms-m.html

Best
Krish

On Nov 17, 2009, at 5:21 PM, Dankner, Nathan (NIH/NIMH) [F] wrote:


Unfortunately I'm not running windows.  Are you familiar with any
tricks I can use on a mac?


On 11/17/09 5:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:

If you're creating the file in windows, try running dos2unix on the
file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:

Hi all,

I am attempting to create a qdec.table.dat file, and have been
unable to find a way to paste my data into it in a way that will
make it readable.  When I paste it in qdec always outputs an error
when trying to open it, even if visually the file appears to be
correct.  Is there an easy way to import data from excel into
something readable by qdec?  I'm hoping to avoid having to manually
enter everything because there is quite a lot of data, so any help
would be appreciated.  Thanks,

Nathan

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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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[Freesurfer] qdec Table Loading Error

[James N. Porter]

Hello-

I'm getting a rather nondescript message of Error loading the data 
table when I try to load my qdec.table.dat into the qdec GUI. I've 
tried using Excel, OpenOffice Calc, OpenOffice Wordprocessor, and Kate 
to save my table as a tab-delimited text file. Nothing works. Any 
suggestions on where I can go next to get a table in the proper format 
for qdec to read?


--
Jim Porter
Graduate Student
Clinical Science  Psychopathology Research
University of Minnesota


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