Hi Tori
the --statsfile option is now --stats i.e use --stats <stats file
name> That in conjuction with --subdir will work.
I'll update the documentation ( which still says --statsfile and is
wrong... sorry! )let me know how it goes.
Thanks
Krish
On Apr 8, 2009, at 10:36 AM, Victoria Williams wrote:
Hello,
I am having a bit of trouble using asegstats2table. I have tried
using different versions of this command and if only I could combine
the two, it would work perfectly. I am trying to compile wmparc
stats for about 160 subjects.
Unlike the new aparcstats2table, asegstats2table seems to not have
the capacity to only report segmentations common to all subjects.
Therefore, I end up with about 160 subjects with unmatching columns
in the table. The first version of asegstats2table I tried was v 1.8
in my stable4 environment. This version allowed me to specify the --
statsfile as wmparc.stats. However, I could not exclude
segmentations such as the wm-hypointensities that was not common to
all subjects and was messing up my table.
The newer 1.20 version in the dev environment does let me specify --
no-segno, however it is not recognizing the --statsfile flag
although it is mentioned in the usage, and gives the following error:
leia:tori:~[82] asegstats2table --version
$Id: asegstats2table,v 1.20 2009/04/07 18:18:09 krish Exp $
leia:tori:CVRAM[87] asegstats2table --subjects CVRAM_001_recon
CVRAM_002_recon CVRAM_003_recon CVRAM_004_recon CVRAM_005_recon
CVRAM_006_recon CVRAM_007_recon CVRAM_008_recon CVRAM_009_recon
CVRAM_010_recon CVRAM_011_recon CVRAM_012_recon CVRAM_013_recon
CVRAM_014_recon CVRAM_016_recon CVRAM_017_recon CVRAM_018_recon
CVRAM_019_recon CVRAM_020_recon CVRAM_021_recon CVRAM_022_recon
CVRAM_023_recon CVRAM_024_recon CVRAM_025_recon CVRAM_026_recon
CVRAM_027_recon CVRAM_028_recon CVRAM_029_recon CVRAM_030_recon
CVRAM_031_recon CVRAM_032_recon CVRAM_033_recon CVRAM_034_recon
CVRAM_035_recon CVRAM_036_recon CVRAM_037_recon CVRAM_038_recon
CVRAM_040_recon CVRAM_041_recon CVRAM_042_recon CVRAM_043_recon
CVRAM_044_recon CVRAM_045_recon CVRAM_046_recon CVRAM_047_recon
CVRAM_048_recon CVRAM_050_recon CVRAM_051_recon CVRAM_052_recon
CVRAM_053_recon CVRAM_054_recon CVRAM_055_recon CVRAM_057_recon
CVRAM_058_recon CVRAM_059_recon CVRAM_060_recon CVRAM_061_recon
CVRAM_062_recon CVRAM_063_recon CVRAM_064_recon CVRAM_066_recon
CVRAM_067_recon CVRAM_068_recon CVRAM_069_recon CVRAM_070_recon
CVRAM_072_recon CVRAM_073_recon CVRAM_074_recon CVRAM_075_recon
CVRAM_076_recon CVRAM_077_recon CVRAM_078_recon CVRAM_079_recon
CVRAM_080_recon CVRAM_081_recon CVRAM_082_recon CVRAM_083_recon
CVRAM_084_recon CVRAM_085_recon CVRAM_086_recon CVRAM_087_recon
CVRAM_089_recon CVRAM_090_recon CVRAM_091_recon CVRAM_092_recon
CVRAM_093_recon CVRAM_095_recon CVRAM_096_recon CVRAM_097_recon
CVRAM_098_recon CVRAM_099_recon CVRAM_100_recon CVRAM_101_recon
CVRAM_103_recon CVRAM_104_recon CVRAM_1045_recon CVRAM_1046_recon
CVRAM_105_recon CVRAM_106_recon CVRAM_108_recon CVRAM_109_recon
CVRAM_111_recon CVRAM_112_recon CVRAM_113_recon CVRAM_114_recon
CVRAM_115_recon CVRAM_117_recon CVRAM_118_recon CVRAM_119_recon
CVRAM_120_recon CVRAM_121_recon CVRAM_122_recon CVRAM_124_recon
CVRAM_125_recon CVRAM_126_recon CVRAM_127_recon CVRAM_128_recon
CVRAM_129_recon CVRAM_130_recon CVRAM_131_recon CVRAM_132_recon
CVRAM_133_recon CVRAM_135_recon CVRAM_136_recon CVRAM_138_recon
CVRAM_139_recon CVRAM_140_recon CVRAM_142_recon CVRAM_143_recon
CVRAM_144_recon CVRAM_145_recon CVRAM_146_recon CVRAM_147_recon
CVRAM_148_recon CVRAM_149_recon CVRAM_151_recon CVRAM_152_recon
CVRAM_153_recon CVRAM_154_recon CVRAM_155_recon CVRAM_156_recon
CVRAM_157_recon CVRAM_158_recon CVRAM_159_recon --no-segno 77 78 79
80 81 82 --subdir stats --statsfile wmparc-nonzero.stats --tablefile
STATS2/stats_tables-cvram/WMparc_stats_nonzero_04082009.txt
asegstats2table: error: no such option: --statsfile
I also tried this:
leia:tori:CVRAM[88] asegstats2table --subjects CVRAM_001_recon
CVRAM_002_recon CVRAM_003_recon CVRAM_004_recon CVRAM_005_recon
CVRAM_006_recon CVRAM_007_recon CVRAM_008_recon CVRAM_009_recon
CVRAM_010_recon CVRAM_011_recon CVRAM_012_recon CVRAM_013_recon
CVRAM_014_recon CVRAM_016_recon CVRAM_017_recon CVRAM_018_recon
CVRAM_019_recon CVRAM_020_recon CVRAM_021_recon CVRAM_022_recon
CVRAM_023_recon CVRAM_024_recon CVRAM_025_recon CVRAM_026_recon
CVRAM_027_recon CVRAM_028_recon CVRAM_029_recon CVRAM_030_recon
CVRAM_031_recon CVRAM_032_recon CVRAM_033_recon CVRAM_034_recon
CVRAM_035_recon CVRAM_036_recon CVRAM_037_recon CVRAM_038_recon
CVRAM_040_recon CVRAM_041_recon CVRAM_042_recon CVRAM_043_recon
CVRAM_044_recon CVRAM_045_recon CVRAM_046_recon CVRAM_047_recon
CVRAM_048_recon CVRAM_050_recon CVRAM_051_recon CVRAM_052_recon
CVRAM_053_recon CVRAM_054_recon CVRAM_055_recon CVRAM_057_recon
CVRAM_058_recon CVRAM_059_recon CVRAM_060_recon CVRAM_061_recon
CVRAM_062_recon CVRAM_063_recon CVRAM_064_recon CVRAM_066_recon
CVRAM_067_recon CVRAM_068_recon CVRAM_069_recon CVRAM_070_recon
CVRAM_072_recon CVRAM_073_recon CVRAM_074_recon CVRAM_075_recon
CVRAM_076_recon CVRAM_077_recon CVRAM_078_recon CVRAM_079_recon
CVRAM_080_recon CVRAM_081_recon CVRAM_082_recon CVRAM_083_recon
CVRAM_084_recon CVRAM_085_recon CVRAM_086_recon CVRAM_087_recon
CVRAM_089_recon CVRAM_090_recon CVRAM_091_recon CVRAM_092_recon
CVRAM_093_recon CVRAM_095_recon CVRAM_096_recon CVRAM_097_recon
CVRAM_098_recon CVRAM_099_recon CVRAM_100_recon CVRAM_101_recon
CVRAM_103_recon CVRAM_104_recon CVRAM_1045_recon CVRAM_1046_recon
CVRAM_105_recon CVRAM_106_recon CVRAM_108_recon CVRAM_109_recon
CVRAM_111_recon CVRAM_112_recon CVRAM_113_recon CVRAM_114_recon
CVRAM_115_recon CVRAM_117_recon CVRAM_118_recon CVRAM_119_recon
CVRAM_120_recon CVRAM_121_recon CVRAM_122_recon CVRAM_124_recon
CVRAM_125_recon CVRAM_126_recon CVRAM_127_recon CVRAM_128_recon
CVRAM_129_recon CVRAM_130_recon CVRAM_131_recon CVRAM_132_recon
CVRAM_133_recon CVRAM_135_recon CVRAM_136_recon CVRAM_138_recon
CVRAM_139_recon CVRAM_140_recon CVRAM_142_recon CVRAM_143_recon
CVRAM_144_recon CVRAM_145_recon CVRAM_146_recon CVRAM_147_recon
CVRAM_148_recon CVRAM_149_recon CVRAM_151_recon CVRAM_152_recon
CVRAM_153_recon CVRAM_154_recon CVRAM_155_recon CVRAM_156_recon
CVRAM_157_recon CVRAM_158_recon CVRAM_159_recon --no-segno 77 78 79
80 81 82 --subdir stats/wmparc-nonzero.stats --tablefile STATS2/
stats_tables-cvram/WMparc_stats_nonzero_04082009.txt
Building the table..
SUBJECTS_DIR : /autofs/space/lang_012/users/CVRAM
ERROR: cannot find /autofs/space/lang_012/users/CVRAM/
CVRAM_001_recon/stats/wmparc-nonzero.stats/aseg.stats
Use --skip flag if you want to continue in such cases
So, it seems that it recognizes the --subdir flag, but is still
looking for aseg.stats instead of a specified statsfile. Does anyone
have any suggestions?
Thanks!
Tori
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