External Email - Use Caution
Dear Dr.Dougla,
Thanks for your reply! I also feel confused, that SUBJECTS_DIR is set
on the the path :/usr/local/freesurfer/subjects and my subjects are indeed on
this path.
------------------ Original ------------------
From: "Greve, Douglas N.,Ph.D."<dgr...@mgh.harvard.edu>;
Date: Mon, Aug 19, 2019 09:32 PM
To: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>;
Subject: Re: [Freesurfer] question about qdec
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:
External Email - Use Caution
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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