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 <lsolom...@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 <lsolom...@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 <
>> gr...@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"
>>> >
>>> -------------------------------------------------------------------------------------------------------
>>> >
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
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>>> but does not contain patient information, please contact the sender and
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>>> dispose of the e-mail.
>>>
>>>
>>
>>
>>
>>
>
>
> --
> 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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