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