if the first run of asegstats2table to table worked, but the second failed, then that means that something is wrong with the stats data for subject 'test1' (or possibly something unusual with the way it was parsed). can you send me the aseg.stats files for both subjects.
for the qcache command: recon-all -s <subjid> -qcache you need to run this for each subject. multiple subjects cannot be included on the command line. per your question on the meaning of 'concatenate into one file', this means that just prior to running mri_glmfit (which qdec does for you) it gathers the data (say, thickness) for each subject under study and combines into a single file. this is just an implementation thing (its easier to process with our software, rather than reading each file individually). n. On Sat, 2009-12-19 at 11:29 +0800, liyari5018 wrote: > Hi, > > Thanks for your reply, I tried to run > > > > asegstats2table --meas volume \ > --tablefile chen.out --subjects chen_yu_an > > > and then: > > > > asegstats2table --meas volume \ > --tablefile test1.out --subjects test1 > > The fisrst conmmand works, and another is failure. > > Report like this: > > --------------------------------------------------------------------- > > FREESURFER_HOME: /usr/local/freesurfer > > Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 > > Debian version: squeeze/sid > > Kernel info: Linux 2.6.31-14-generic i686 > > --------------------------------------------------------------------- > > 1) test1 chen_yu_an > > 2) > > lijin-desktop:/usr/local/freesurfer/subjects# python -V > > Python 2.6.4 > > ------------------------------------------------------------------------------------------------------ > > lijin-desktop:/usr/local/freesurfer/subjects# uname -a > > Linux lijin-desktop 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 > 14:04:26 UTC 2009 i686 GNU/Linux > > 3) > > ============================================================ > > lijin-desktop:/usr/local/freesurfer/subjects# asegstats2table --meas > volume --tablefile chen.out --subjects chen_yu_an > > /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the > sets module is deprecated > > from sets import Set > > Building the table.. > > SUBJECTS_DIR : /usr/local/freesurfer/subjects > > Writing the table to chen.out > > ------------------------------------------------------------------------------------------------------ > > lijin-desktop:/usr/local/freesurfer/subjects# asegstats2table --meas > volume --tablefile test1.out --subjects test1 > > /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the > sets module is deprecated > > from sets import Set > > Building the table.. > > SUBJECTS_DIR : /usr/local/freesurfer/subjects > > Traceback (most recent call last): > > File "/usr/local/freesurfer/bin/asegstats2table", line 406, in > <module> > > (rows, cols, table) = build_table(options) > > File "/usr/local/freesurfer/bin/asegstats2table", line 322, in > build_table > > table[statno+subname][segid] = > float(strlst[seg2statcol_map[o.meas]]) > > ValueError: invalid literal for float(): Volume_mm3 > > ======================================================= > > --------------------------------------------------------------------- > > Please include the following additional information in your report: > > 1) subject name > > 2) the entire command-line executed > > 3) the error message generated > > 4) optionally include the subject's /script/recon-all.log > > ----------------------------------------------------------------------- > > And one mroe quesitons: > > When I start Qdec befor, Qdec needs each subject to have pre-computed > smoothed data for the target surface (fsaverage is the default) for > each measure (thickness, sulc, area, curv, etc.), and in the > "pre-smoothed fsaverage surfaces" part , I CAN'T understand the > command: > > > > recon-all -s <subjid> -qcache > > The conmmand has three functions as the tutorial ppt show: > > 1\Resample into Common Space > > 2\Smooth > > 3\Concatenate into one file <<<<< What does this mean??? > > should I run this conmmand like this: > > # recon-all -s test1 -qcache > > # rcon-all -s chen_yu_an -qcache > > or like this: > > # recon-all -s test1 chen_yu_an -qcache > > > Thanks again for your reply! > > LJ > > > > > 在2009-12-19，"Nick Schmansky" <ni...@nmr.mgh.harvard.edu> 写道： > >from the error output shown, the problem appears to occur in the > >aparcstats2table script (line 322). its failing to parse a float. > > > >which version of freesurfer is being used? (type 'bugr' for this info) > >and which version of python? (type 'python -V') > > > >also, try running: > > > >asegstats2table --meas volume \ > > --tablefile test1.out --subjects test1 > > > >and then: > > > >asegstats2table --meas volume \ > > --tablefile chen.out --subjects chen_yu_an > > > >and see if either one works. i suspect either the aseg.stats file in > >one or the other is corrupted, or there's a problem with the python > >version on your system (its known to work with python v2.3.4). > > > >n. > > > > > > > >On Fri, 2009-12-18 at 19:12 +0800, liyari5018 wrote: > >> Hi all, > >> What's wrong with my QDEC? Today, I use the FeeSurfer Tutorial: > >> Surface Group Analysis with Qdec to analysis my data , when I > >> carried out to '' Stats Data Import'', I press the 'Generate Stats > >> Data Tables' button, but something happend to with a error(red > >> letters ): > >> > >> mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/ > >> > >> ---------------------------------------------------------- > >> asegstats2table --meas volume > >> --tablefile > >> /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat > >> --subjects test1 chen_yu_an > >> /usr/local/freesurfer/bin/asegstats2table:5: DeprecationWarning: the > >> sets module is deprecated > >> from sets import Set > >> Building the table.. > >> SUBJECTS_DIR : /usr/local/freesurfer/subjects > >> Traceback (most recent call last): > >> File "/usr/local/freesurfer/bin/asegstats2table", line 406, in > >> <module> > >> (rows, cols, table) = build_table(options) > >> File "/usr/local/freesurfer/bin/asegstats2table", line 322, in > >> build_table > >> table[statno+subname][segid] = > >> float(strlst[seg2statcol_map[o.meas]]) > >> ValueError: invalid literal for float(): Volume_mm3 > >> ERROR: > >> In /usr/pubsw/packages/KWWidgets/CVS/src/KWWidgets/vtkKWTkUtilities.cxx, > >> line 230 > >> vtkKWQdecApp (0xa562cb8): > >> Script: > >> vtkTemp3 GenerateStatsDataTables > >> Returned Error on line 1: > >> Uncaught exception: command failed: asegstats2table --meas volume > >> --tablefile > >> /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat > >> --subjects test1 chen_yu_an > >> > >> Stack trace: > >> Uncaught exception: command failed: asegstats2table --meas volume > >> --tablefile > >> /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat > >> --subjects test1 chen_ yu_an > >> > >> while executing > >> "vtkTemp3 GenerateStatsDataTables" > >> > >> > >> What does this mean? How do I do to solve this ???? > >> > >> Thank you > >> > >> LJ > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> 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
