It looks like your SUBJECTS_DIR is set to the wrong place. It should be set to the folder where ever your subjects (eg, PT1_01) are
On 8/19/2019 4:45 AM, 310913949 wrote:
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Hi FS Experts, I meet some problem when I use QDEC for Group analysis. When I click Generate Stats Data Tables, it report the errors as follows: dec/gender.levels Female Male done. Reading discrete factor levels from config file /usr/local/freesurfer/subjects/qdec/diagnosis.levels TLE extra_TLE done.
Data table /usr/local/freesurfer/subjects/qdec/qdec.table.dat loaded. Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_01' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_03' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_04' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_06' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_11' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_12' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_14' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_47' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_55' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_05' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_16' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_18' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_20' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_23' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_24' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_40' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'PT1_75' in SUBJECTS_DIR Input table: /usr/local/freesurfer/subjects/qdec/qdec.table.dat Subj#, SubjID, Data... 1 PT1_01 Female 23.000000 TLE 2 PT1_03 Male 38.000000 TLE 3 PT1_04 Male 26.000000 TLE 4 PT1_06 Female 45.000000 TLE 5 PT1_11 Female 20.000000 TLE 6 PT1_12 Male 23.000000 TLE 7 PT1_14 Female 39.000000 TLE 8 PT1_47 Female 30.000000 TLE 9 PT1_55 Female 22.000000 TLE 10 PT1_05 Male 42.000000 extra_TLE 11 PT1_16 Female 34.000000 extra_TLE 12 PT1_18 Male 30.000000 extra_TLE 13 PT1_20 Male 40.000000 extra_TLE 14 PT1_23 Male 30.000000 extra_TLE 15 PT1_24 Female 29.000000 extra_TLE 16 PT1_40 Male 30.000000 extra_TLE 17 PT1_75 Female 24.000000 extra_TLE 1 gender discrete 2 1 Female 2 Male 2 age continuous 0 3 diagnosis discrete 2 1 TLE 2 extra_TLE Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 30.882 7.631
Number of subjects: 17 Number of factors: 3 (2 discrete, 1 continuous) Number of classes: 4 Number of regressors: 8 ============================================================ Data table loading completed successfully. SUBJECTS_DIR is '/usr/local/freesurfer/subjects' mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/
---------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects PT1_01 PT1_03 PT1_04 PT1_06 PT1_11 PT1_12 PT1_14 PT1_47 PT1_55 PT1_05 PT1_16 PT1_18 PT1_20 PT1_23 PT1_24 PT1_40 PT1_75 File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax
I have read some answer in the freesurfer mailing list, but I still don't know how to deal with it. Could you please give me some suggestion? Thanks, Kan
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