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
test1 chen_yu_an
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
============================================================
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:
subject name
the entire command-line executed
the error message generated
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" nicks@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
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