Hi Douglas,

I get the same error for every subject individually. I'm guessing there is a problem with my aseg.stats files but when I look through them they look okay to me. What would be the best way to identify the problem?

Thank you!
LS 

On Mon, Feb 22, 2016 at 11:18 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Not sure. Can you run it separately for each subject? I suspect that
there might be a subject with a bad stats file

On 02/19/2016 02:58 PM, levi solomyak wrote:
> Hi Douglas,
>
> Sure! Below is the terminal outputs when I try and run the command you
> suggested on the first five subjects. Any help you could provide would
> be much appreciated!
>
> Best,
> LS
>
>  $asegstats2table --common-segs --meas volume --tablefile
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
> SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/Applications/freesurfer/bin/asegstats2table", line 538, in
> <module>
>     id_name_map, measurelist = parsed.parse(options.meas)
>   File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
>
> On Fri, Feb 19, 2016 at 2:53 PM, levi solomyak <lsolomyak@gmail.com
> <mailto:lsolomyak@gmail.com>> wrote:
>
>     Hi Douglas,
>
>     Sure! Below is the terminal outputs when I try and run the command
>     you suggested on the first five subjects. Any help you could
>     provide would be much appreciated!
>
>     Best,
>     LS
>
>      $asegstats2table --common-segs --meas volume --tablefile
>     /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>     --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411
>     SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
>     Parsing the .stats files
>     Traceback (most recent call last):
>       File "/Applications/freesurfer/bin/asegstats2table", line 538,
>     in <module>
>         id_name_map, measurelist = parsed.parse(options.meas)
>       File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse
>
>     On Fri, Feb 19, 2016 at 2:47 PM, levi solomyak
>     <lsolomyak@gmail.com <mailto:lsolomyak@gmail.com>> wrote:
>
>         Hi Douglas,
>
>         Sure! Below is the terminal outputs when I try and run the
>         command you suggested on the first five subjects. Any help you
>         could provide would be much appreciated!
>
>         Best,
>         LS
>
>          $asegstats2table --common-segs --meas volume --tablefile
>         /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>         --statsfile=aseg.stats --subjects 100307 101006 104820 105115
>         110411
>         SUBJECTS_DIR : /projects/IndivRITL/data/leviDiff/Subjects
>         Parsing the .stats files
>         Traceback (most recent call last):
>           File "/Applications/freesurfer/bin/asegstats2table", line
>         538, in <module>
>             id_name_map, measurelist = parsed.parse(options.meas)
>           File "/Applications/freesurfer/bin/fsutils.py", line 115, in
>         parse
>             self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
>         IndexError: list index out of range
>
>
>
>         On Mon, Dec 21, 2015 at 6:13 PM, Douglas N Greve
>         <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>         wrote:
>
>             Can you run the command below outside of qdec and send us
>             the error it
>             prints to the terminal?
>
>             asegstats2table --common-segs --meas volume --tablefile
>             /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>             --statsfile=aseg.stats --subjects 100307 101006 104820
>             105115 110411
>             111312 111413 111716 112819 113215 113619 113922 114419
>             115320 116524
>             117122 117324 118528 135225 135932 150625 150726 151223
>             151526 170934
>             171633 172130 172332 172534 172938 173334 175439 177645
>             177746 178142
>             200109 200614 201111 201414 201818 203418 204016 204521
>             304020 307127
>             308331 310621 316633 329440 365343 366042 377451 380036
>             385450 386250
>             412528 433839 436239 480141 486759 497865 499566 500222
>             510326 530635
>             531536 540436 561242 562446 565452 566454 567052 567961
>             568963 571548
>             580044 580347 581349 583858 586460 594156 598568 599671
>
>
>
>             On 12/14/2015 02:15 PM, levi solomyak wrote:
>             > Dear experts,
>             >
>             > I've been attempting to generate a stats data table in
>             qdec, but each
>             > time I get a "Index Error: list index is out of range"
>             error. This is
>             > occurring when it is trying to parse the .stats file.
>             >
>             >  I've made sure that the files all line up exactly with
>             the qdec table
>             > and that SUBJECTS_DIR  is properly sourced so I'm not
>             sure how to fix
>             > this problem. Any help would be greatly appreciated!
>             >
>             >
>             > Here are the details of the errors:
>             >
>             > 1) machine being used: Linux localhost.localdomain
>             > 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC
>             2015 x86_64
>             > x86_64 x86_64 GNU/Linux
>             > 2) Freesurfer version:
>             > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
>             > 3) Current working directory:
>             /projects/IndivRITL/data/leviDiff/Subjects
>             > 4) which qdec : /usr/local/freesurfer/bin/qdec
>             > 5) After loading the gui, I attempted to generate a qdec
>             stats table.
>             > This is the error that was returned:
>             >
>             >
>             -----------------------------------------------------------------------------------
>             > asegstats2table --common-segs --meas volume --tablefile
>             >
>             /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>             > --statsfile=aseg.stats --subjects 100307 101006 104820
>             105115 110411
>             > 111312 111413 111716 112819 113215 113619 113922 114419
>             115320 116524
>             > 117122 117324 118528 135225 135932 150625 150726 151223
>             151526 170934
>             > 171633 172130 172332 172534 172938 173334 175439 177645
>             177746 178142
>             > 200109 200614 201111 201414 201818 203418 204016 204521
>             304020 307127
>             > 308331 310621 316633 329440 365343 366042 377451 380036
>             385450 386250
>             > 412528 433839 436239 480141 486759 497865 499566 500222
>             510326 530635
>             > 531536 540436 561242 562446 565452 566454 567052 567961
>             568963 571548
>             > 580044 580347 581349 583858 586460 594156 598568 599671
>             > SUBJECTS_DIR :
>             /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects
>             > Parsing the .stats files
>             > Traceback (most recent call last):
>             >   File "/usr/local/freesurfer/bin/asegstats2table", line
>             538, in <module>
>             >     id_name_map, measurelist = parsed.parse(options.meas)
>             >   File "/home/usr/local/freesurfer/bin/fsutils.py", line
>             115, in parse
>             >     self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
>             > IndexError: list index out of range
>             > ERROR: In
>             >
>             /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
>             > line 230
>             > vtkKWQdecApp (0x278d8060):
>             >     Script:
>             > vtkTemp2 GenerateStatsDataTables
>             >     Returned Error on line 1:
>             > Uncaught exception: command failed: asegstats2table
>             --common-segs
>             > --meas volume --tablefile
>             >
>             /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>             > --statsfile=aseg.stats --subjects 100307 101006 104820
>             105115 110411
>             > 111312 111413 111716 112819 113215 113619 113922 114419
>             115320 116524
>             > 117122 117324 118528 135225 135932 150625 150726 151223
>             151526 170934
>             > 171633 172130 172332 172534 172938 173334 175439 177645
>             177746 178142
>             > 200109 200614 201111 201414 201818 203418 204016 204521
>             304020 307127
>             > 308331 310621 316633 329440 365343 366042 377451 380036
>             385450 386250
>             > 412528 433839 436239 480141 486759 497865 499566 500222
>             510326 530635
>             > 531536 540436 561242 562446 565452 566454 567052 567961
>             568963 571548
>             > 580044 580347 581349 583858 586460 594156 598568 599671
>             >
>             > Stack trace:
>             > Uncaught exception: command failed: asegstats2table
>             --common-segs
>             > --meas volume --tablefile
>             >
>             /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>             > --statsfile=aseg.stats --subjects 100307 101006 104820
>             105115 110411
>             > 111312 111413 111716 112819 113215 113619 113922 114419
>             115320 116524
>             > 117122 117324 118528 135225 135932 150625 150726 151223
>             151526 170934
>             > 171633 172130 172332 172534 172938 173334 175439 177645
>             177746 178142
>             > 200109 200614 201111 201414 201818 203418 204016 204521
>             304020 307127
>             > 308331 310621 316633 329440 365343 366042 377451 380036
>             385450 386250
>             > 412528 433839 436239 480141 486759 497865 499566 500222
>             510326 530635
>             > 531536 540436 561242 562446 565452 566454 567052 567961
>             568963 571548
>             > 580044 580347 581349 583858 586460 594156 598568 599671
>             >
>             >     while executing
>             > "vtkTemp2 GenerateStatsDataTables"
>             >
>             -------------------------------------------------------------------------------------------------------
>             >
>             >
>             >
>             >
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>
>             --
>             Douglas N. Greve, Ph.D.
>             MGH-NMR Center
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>     --
>     Levi Solomyak
>     Cole Neuroscience Laboratory (_colelab.org <http://colelab.org/>_)
>     Center for Molecular and Behavioral Neuroscience (CMBN)
>     Rutgers-Newark University
>
>
>
>
> --
> Levi Solomyak
> Cole Neuroscience Laboratory (_colelab.org <http://colelab.org/>_)
> Center for Molecular and Behavioral Neuroscience (CMBN)
> Rutgers-Newark University
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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