22 Feb
2016
22 Feb
'16
3:42 p.m.
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 <greve@nmr.mgh.harvard.edu mailto: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> > <mailto: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> <mailto: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> <mailto: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" > > > ------------------------------------------------------------------------------------------------------- > > > > > > > > > > _______________________________________________ > > 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 > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
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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
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/