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help > RE: Run CONN script on the server with java error
May 18, 2022 02:05 PM | nshih
RE: Run CONN script on the server with java error
Hi Alfonso,
It can run now. Thank you!
I have quick question about 'default_mni'. What specific steps included in this pipeline? And which one may try to launch a prompt GUI?
In my original script, I used 'default_mni' as the processing step, and it worked well under the JAVA condition, but it didn't work without JAVA. This is why I try to build my own precessing pipeline.
Best,
Judy
Originally posted by Alfonso Nieto-Castanon:
It can run now. Thank you!
I have quick question about 'default_mni'. What specific steps included in this pipeline? And which one may try to launch a prompt GUI?
In my original script, I used 'default_mni' as the processing step, and it worked well under the JAVA condition, but it didn't work without JAVA. This is why I try to build my own precessing pipeline.
Best,
Judy
Originally posted by Alfonso Nieto-Castanon:
Hi Judy,
Thanks for sharing your script. I believe the issue there is that you are including a 'functional_label' step during preprocessing but not explicitly defining the label that you want to assign to that dataset (so CONN will stop and try to launch a prompt GUI asking you to define that label, which naturally fails since the server might not have any graphic capabilities or ability to interact with users).
In any case, simply changing the step 'functional_label' to 'functional_label_as_mnispace' (or any more appropriate label that you might want to assign there) should fix this issue
Another unrelated issues is that in your preprocessing pipeline you seem to be selecting the steps:
... 'functional_segment&normalize_direct', ... , 'structural_normalize_preservemasks', 'functional_normalize_direct' ...
but that seems like a strange combination, which, in addition to normalizing your functional data twice, it is also likely going to result in misaligned gray/white/CSF masks. I would perhaps suggest considering instead:
... 'functional_segment&normalize_direct', ... , 'structural_normalize'
or, alternatively, if you just want to use the default MNI pipeline in CONN, you may simply use the single step 'default_mni' instead of an explicit list of preprocessing steps in the Setup.preprocessing.steps field to specify that)
Best
Alfonso
Originally posted by nshih:
Thanks for sharing your script. I believe the issue there is that you are including a 'functional_label' step during preprocessing but not explicitly defining the label that you want to assign to that dataset (so CONN will stop and try to launch a prompt GUI asking you to define that label, which naturally fails since the server might not have any graphic capabilities or ability to interact with users).
In any case, simply changing the step 'functional_label' to 'functional_label_as_mnispace' (or any more appropriate label that you might want to assign there) should fix this issue
Another unrelated issues is that in your preprocessing pipeline you seem to be selecting the steps:
... 'functional_segment&normalize_direct', ... , 'structural_normalize_preservemasks', 'functional_normalize_direct' ...
but that seems like a strange combination, which, in addition to normalizing your functional data twice, it is also likely going to result in misaligned gray/white/CSF masks. I would perhaps suggest considering instead:
... 'functional_segment&normalize_direct', ... , 'structural_normalize'
or, alternatively, if you just want to use the default MNI pipeline in CONN, you may simply use the single step 'default_mni' instead of an explicit list of preprocessing steps in the Setup.preprocessing.steps field to specify that)
Best
Alfonso
Originally posted by nshih:
Hi
Alfonso,
Thanks for your response!
Attached file is my script. I have hundreds of subjects needed to run, so I try to run them under the server's background.
Thanks for your help in advance!
Best,
Judy
Originally posted by Alfonso Nieto-Castanon:
Thanks for your response!
Attached file is my script. I have hundreds of subjects needed to run, so I try to run them under the server's background.
Thanks for your help in advance!
Best,
Judy
Originally posted by Alfonso Nieto-Castanon:
Hi Judy,
Sorry about that, it seems the script is trying to launch a GUI window to ask you to enter the labels for your functional datasets (but that should not be possible whether your server has jvm enabled or not, assuming that your server is just a terminal without graphics). Could you please share your script to see if that gives me a hint as to why that may be happening only when starting without a java virtual machine?
Thanks
Alfonso
Originally posted by nshih:
Sorry about that, it seems the script is trying to launch a GUI window to ask you to enter the labels for your functional datasets (but that should not be possible whether your server has jvm enabled or not, assuming that your server is just a terminal without graphics). Could you please share your script to see if that gives me a hint as to why that may be happening only when starting without a java virtual machine?
Thanks
Alfonso
Originally posted by nshih:
Hi CONN expert,
When I run my CONN script for resting state analysis on server with java, it works totally well. However, when I'm try to run this same script on the server without using no java, I always get error which complaining these line (below) in preprocessing step (I used 'default_mni'). I'm not sure which steps in this 'default_mni' pipeline will using java, and are these steps necessary for resting state analysis? I wonder if java is required for running precessing pipeline on CONN? Or there is the way to figure out this issue?
these are the error I got:
------------------------------------------
Error using warnfiguredialog (line 12)
This functionality is no longer supported under the -nojvm startup option. For
more information, see "Changes to -nojvm Startup Option" in the MATLAB Release
Notes. To view the release note in your system browser, run
web('http://www.mathworks.com/help/matlab/release-notes.html#btsurqv-6',
'-browser').
Error in dialog (line 39)
warnfiguredialog('dialog');
Error in inputdlg (line 141)
InputFig=dialog( ...
Error in conn_setup_preproc (line 817)
label=inputdlg('Enter functional label (arbitrary
description)','conn_setup_preproc',1,label);
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING
SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1236)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
------------------------------------------
Thanks for your help!
Thanks,
Judy
When I run my CONN script for resting state analysis on server with java, it works totally well. However, when I'm try to run this same script on the server without using no java, I always get error which complaining these line (below) in preprocessing step (I used 'default_mni'). I'm not sure which steps in this 'default_mni' pipeline will using java, and are these steps necessary for resting state analysis? I wonder if java is required for running precessing pipeline on CONN? Or there is the way to figure out this issue?
these are the error I got:
------------------------------------------
Error using warnfiguredialog (line 12)
This functionality is no longer supported under the -nojvm startup option. For
more information, see "Changes to -nojvm Startup Option" in the MATLAB Release
Notes. To view the release note in your system browser, run
web('http://www.mathworks.com/help/matlab/release-notes.html#btsurqv-6',
'-browser').
Error in dialog (line 39)
warnfiguredialog('dialog');
Error in inputdlg (line 141)
InputFig=dialog( ...
Error in conn_setup_preproc (line 817)
label=inputdlg('Enter functional label (arbitrary
description)','conn_setup_preproc',1,label);
Error in conn_process (line 27)
case 'setup_preprocessing', conn_disp(['CONN: RUNNING
SETUP.PREPROCESSING STEP']); conn_setup_preproc(varargin{:});
Error in conn_batch (line 1236)
conn_process('setup_preprocessing',steps,'subjects',SUBJECTS,OPTIONS{:});
------------------------------------------
Thanks for your help!
Thanks,
Judy
Threaded View
| Title | Author | Date |
|---|---|---|
| nshih | May 6, 2022 | |
| Alfonso Nieto-Castanon | May 9, 2022 | |
| nshih | May 11, 2022 | |
| Alfonso Nieto-Castanon | May 11, 2022 | |
| nshih | May 18, 2022 | |