can you send one of them? On 02/22/2016 03:13 PM, levi solomyak wrote: > 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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <lsolom...@gmail.com <mailto:lsolom...@gmail.com> > > <mailto:lsolom...@gmail.com <mailto: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 <mailto:lsolom...@gmail.com> > <mailto:lsolom...@gmail.com <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > 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> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > > > > > > > > > > > > > > > -- > > Levi Solomyak > > Cole Neuroscience Laboratory (_colelab.org > <http://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> > <http://colelab.org/>_) > > Center for Molecular and Behavioral Neuroscience (CMBN) > > Rutgers-Newark University > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
