Good afternoon CONN community,
First, thank you to the developers for creating and maintaining this project!
Several of us have shifted as much of our data processing as possible to our cluster (running torque, for now). Although we have been using several versions of both CONN and Matlab, this is specifically using CONN16a and Matlab 2016a.
We would greatly appreciate any input you may have regarding these errors and if the minor code change to get around the second issue is acceptable.
Recently, we ran into a few issues I was hoping to receive some guidance on:
1) When loading conn, the following warnings are thrown:
Warning: Cannot recognise format. Trying Analyze.
> In read_hdr_raw (line 50)
In read_hdr (line 30)
In nifti (line 26)
In spm_vol_nifti (line 19)
In spm_vol>spm_vol_hdr (line 128)
In spm_vol (line 61)
In conn_getinfo (line 18)
In conn (line 606)
In conn (line 105)
Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In mayo2nifti1 (line 63)
In nifti (line 30)
In spm_vol_nifti (line 19)
In spm_vol>spm_vol_hdr (line 128)
In spm_vol (line 61)
In conn_getinfo (line 18)
In conn (line 606)
In conn (line 105)
2) When submitting queue jobs (just tested through the pre-processing so far), the following error is thrown (complete output below):
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016a (9.0.0.341360) 64-bit (glnxa64)
February 11, 2016
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/dastudio/depviewer
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/glue
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/glue/studio
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide/mdlinfo
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide/registry
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide/tfl
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/hdlcoder/slhdltemplates
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/robust/rctguis
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/simulink/sta/report
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/slvnv/reqmgt
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/slvnv/reqmgt/RTExplorer
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/curvefit/cftoolgui
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/system/preferences
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/simulink/simharness/simharness
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/javabuilder/javabuilderdemos
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Academic License
/scratch/lfs/vabfmc/RESEARCH/WM_TBI_EMOTION/resting_analysis/conn_project01.qlog/160509111029936/node.0087160509111029936.sh running
Processing /scratch/lfs/vabfmc/RESEARCH/WM_TBI_EMOTION/resting_analysis/conn_project01.mat?id=0087160509111029936,subjects=87 job 1/1
CONN: RUNNING SETUP.PREPROCESSING STEP
Warning: uiwait is no longer supported when MATLAB is started with the
-nodisplay or -noFigureWindows option or there is no display. For more
information, see "Changes to -nodisplay and -noFigureWindows Startup Options"
in the MATLAB Release Notes. To view the release note in your system browser,
run web('www.mathworks.com/help/matlab/release-notes.html#br5ktrh-3',
'-browser')
> In warnfiguredialog (line 21)
In uiwait (line 40)
In conn_setup_preproc (line 338)
In conn_process (line 22)
In conn_jobmanager (line 423)
------------------------------------------------------------------------------------------------------------------------------------
Tracking this down, it appears that conn is using a modal wait (uiwait) for queue jobs and thus hanging at this point.
To obviate this, I commented out the uiwait at line 423 in conn_jobmanager.m and tried again -- the job then executes successfully, although this may impair the intended function of the gui.
Thank you for your input and advice,
Damon
First, thank you to the developers for creating and maintaining this project!
Several of us have shifted as much of our data processing as possible to our cluster (running torque, for now). Although we have been using several versions of both CONN and Matlab, this is specifically using CONN16a and Matlab 2016a.
We would greatly appreciate any input you may have regarding these errors and if the minor code change to get around the second issue is acceptable.
Recently, we ran into a few issues I was hoping to receive some guidance on:
1) When loading conn, the following warnings are thrown:
Warning: Cannot recognise format. Trying Analyze.
> In read_hdr_raw (line 50)
In read_hdr (line 30)
In nifti (line 26)
In spm_vol_nifti (line 19)
In spm_vol>spm_vol_hdr (line 128)
In spm_vol (line 61)
In conn_getinfo (line 18)
In conn (line 606)
In conn (line 105)
Warning: QFORM0 representation has been rounded.
> In encode_qform0 (line 27)
In mayo2nifti1 (line 63)
In nifti (line 30)
In spm_vol_nifti (line 19)
In spm_vol>spm_vol_hdr (line 128)
In spm_vol (line 61)
In conn_getinfo (line 18)
In conn (line 606)
In conn (line 105)
2) When submitting queue jobs (just tested through the pre-processing so far), the following error is thrown (complete output below):
< M A T L A B (R) >
Copyright 1984-2016 The MathWorks, Inc.
R2016a (9.0.0.341360) 64-bit (glnxa64)
February 11, 2016
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/dastudio/depviewer
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/glue
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/glue/studio
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide/mdlinfo
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide/registry
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/idelink/extensions/eclipseide/tfl
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/hdlcoder/slhdltemplates
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/robust/rctguis
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/simulink/sta/report
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/slvnv/reqmgt
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/slvnv/reqmgt/RTExplorer
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/curvefit/cftoolgui
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/shared/system/preferences
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/simulink/simharness/simharness
Warning: Name is nonexistent or not a directory:
/apps/matlab/r2016a/toolbox/javabuilder/javabuilderdemos
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
Academic License
/scratch/lfs/vabfmc/RESEARCH/WM_TBI_EMOTION/resting_analysis/conn_project01.qlog/160509111029936/node.0087160509111029936.sh running
Processing /scratch/lfs/vabfmc/RESEARCH/WM_TBI_EMOTION/resting_analysis/conn_project01.mat?id=0087160509111029936,subjects=87 job 1/1
CONN: RUNNING SETUP.PREPROCESSING STEP
Warning: uiwait is no longer supported when MATLAB is started with the
-nodisplay or -noFigureWindows option or there is no display. For more
information, see "Changes to -nodisplay and -noFigureWindows Startup Options"
in the MATLAB Release Notes. To view the release note in your system browser,
run web('www.mathworks.com/help/matlab/release-notes.html#br5ktrh-3',
'-browser')
> In warnfiguredialog (line 21)
In uiwait (line 40)
In conn_setup_preproc (line 338)
In conn_process (line 22)
In conn_jobmanager (line 423)
------------------------------------------------------------------------------------------------------------------------------------
Tracking this down, it appears that conn is using a modal wait (uiwait) for queue jobs and thus hanging at this point.
To obviate this, I commented out the uiwait at line 423 in conn_jobmanager.m and tried again -- the job then executes successfully, although this may impair the intended function of the gui.
Thank you for your input and advice,
Damon