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help > Tools > Run > Setup/Denoising/1st-level analyses broken in CONN 18b
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May 22, 2019 03:05 PM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
Tools > Run > Setup/Denoising/1st-level analyses broken in CONN 18b
Dear Alfonso,
I have run multiple times into a peculiar issue, which probably needs only a minor fix.
In CONN 18b, the "Tools > Run > Setup/Denoising/1st-level analyses" util that I often use to run the whole pipeline at once is stopping in CONN 18b with this error:
ERROR DESCRIPTION:
This error arise in the Setup step directly. It happened on all analyses I tried to run with CONN 18b. Running the step by clicking the "Done" button instead works. This error does not happen with CONN 18a nor CONN 17f, on the same datasets and projects and configuration (I am using my script that interfaces with conn_batch.m, so that I can ensure that the same parameters are set).
Thank you for your help in advance,
Best regards,
Stephen
I have run multiple times into a peculiar issue, which probably needs only a minor fix.
In CONN 18b, the "Tools > Run > Setup/Denoising/1st-level analyses" util that I often use to run the whole pipeline at once is stopping in CONN 18b with this error:
ERROR DESCRIPTION:
Error using conn_process (line 2027)
Some conditions have not been processed yet. Re-run previous step
Some conditions have not been processed yet. Re-run previous step
Error in conn_process (line 44)
case 'analyses_gui_seedandroi',conn_disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10,11,15],varargin{:});
case 'analyses_gui_seedandroi',conn_disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10,11,15],varargin{:});
Error in conn (line 1438)
conn_process(psteps{CONN_x.gui.processes{1}(n)},CONN_x.gui.processes{2}{n});
conn_process(psteps{CONN_x.gui.processes{1}(n)},CONN_x.gui.processes{2}{n});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + DEM FieldMap LST MEEGtools StabMultip cat12 ns rsHRF
Matlab v.2018a
project: CONN18.b
storage: 1353.2Gb available
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + DEM FieldMap LST MEEGtools StabMultip cat12 ns rsHRF
Matlab v.2018a
project: CONN18.b
storage: 1353.2Gb available
spm @ C:\matlab_tools\spm12
conn @ C:\matlab_tools\conn18b
conn @ C:\matlab_tools\conn18b
This error arise in the Setup step directly. It happened on all analyses I tried to run with CONN 18b. Running the step by clicking the "Done" button instead works. This error does not happen with CONN 18a nor CONN 17f, on the same datasets and projects and configuration (I am using my script that interfaces with conn_batch.m, so that I can ensure that the same parameters are set).
Thank you for your help in advance,
Best regards,
Stephen
May 25, 2019 05:05 PM | Alfonso Nieto-Castanon - Boston University
RE: Tools > Run > Setup/Denoising/1st-level analyses broken in CONN 18b
Dear Stephen,
Thank you very much for reporting this issue. Please try the attached patch and let me know if you still run into any issues (this patch is for release 18b, to install it copy the attached file to your conn distribution folder overwriting the file with the same name there)
Thanks again!
Alfonso
Originally posted by Stephen L.:
Thank you very much for reporting this issue. Please try the attached patch and let me know if you still run into any issues (this patch is for release 18b, to install it copy the attached file to your conn distribution folder overwriting the file with the same name there)
Thanks again!
Alfonso
Originally posted by Stephen L.:
Dear Alfonso,
I have run multiple times into a peculiar issue, which probably needs only a minor fix.
In CONN 18b, the "Tools > Run > Setup/Denoising/1st-level analyses" util that I often use to run the whole pipeline at once is stopping in CONN 18b with this error:
ERROR DESCRIPTION:
This error arise in the Setup step directly. It happened on all analyses I tried to run with CONN 18b. Running the step by clicking the "Done" button instead works. This error does not happen with CONN 18a nor CONN 17f, on the same datasets and projects and configuration (I am using my script that interfaces with conn_batch.m, so that I can ensure that the same parameters are set).
Thank you for your help in advance,
Best regards,
Stephen
I have run multiple times into a peculiar issue, which probably needs only a minor fix.
In CONN 18b, the "Tools > Run > Setup/Denoising/1st-level analyses" util that I often use to run the whole pipeline at once is stopping in CONN 18b with this error:
ERROR DESCRIPTION:
Error using conn_process (line 2027)
Some conditions have not been processed yet. Re-run previous step
Some conditions have not been processed yet. Re-run previous step
Error in conn_process (line 44)
case 'analyses_gui_seedandroi',conn_disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10,11,15],varargin{:});
case 'analyses_gui_seedandroi',conn_disp(['CONN: RUNNING ANALYSIS STEP (ROI-to-ROI or seed-to-voxel analyses)']); conn_process([10,11,15],varargin{:});
Error in conn (line 1438)
conn_process(psteps{CONN_x.gui.processes{1}(n)},CONN_x.gui.processes{2}{n});
conn_process(psteps{CONN_x.gui.processes{1}(n)},CONN_x.gui.processes{2}{n});
Error in conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + DEM FieldMap LST MEEGtools StabMultip cat12 ns rsHRF
Matlab v.2018a
project: CONN18.b
storage: 1353.2Gb available
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN18.b
SPM12 + DEM FieldMap LST MEEGtools StabMultip cat12 ns rsHRF
Matlab v.2018a
project: CONN18.b
storage: 1353.2Gb available
spm @ C:\matlab_tools\spm12
conn @ C:\matlab_tools\conn18b
conn @ C:\matlab_tools\conn18b
This error arise in the Setup step directly. It happened on all analyses I tried to run with CONN 18b. Running the step by clicking the "Done" button instead works. This error does not happen with CONN 18a nor CONN 17f, on the same datasets and projects and configuration (I am using my script that interfaces with conn_batch.m, so that I can ensure that the same parameters are set).
Thank you for your help in advance,
Best regards,
Stephen
Jul 9, 2019 01:07 PM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
RE: Tools > Run > Setup/Denoising/1st-level analyses broken in CONN 18b
Dear Alfonso,
Thank you very much for this patch, and sorry for the delay, I did not have the opportunity to run an analysis since then.
I tested the patch and it half works: the analyses are indeed done, but it seems they are not properly registered in the project, as clicking on 1st-level or 2nd-level tabs will raise an error which I don't recall the exact phrasing but something like "The analysis is not ready, please run denoising first". If I then go back to Denoising, click on Done, and select to skip already preprocessed seeds/subjects, then all the calculations are very fast as it probably just skips everything but then the 1st analysis is working.
Not sure if it can help, but I attach the log for this analysis (there is only one subject BTW).
Let me know if I can provide you with any additional helpful information, and thank you very much for taking the time to look into this issue,
Best regards,
Stephen
Thank you very much for this patch, and sorry for the delay, I did not have the opportunity to run an analysis since then.
I tested the patch and it half works: the analyses are indeed done, but it seems they are not properly registered in the project, as clicking on 1st-level or 2nd-level tabs will raise an error which I don't recall the exact phrasing but something like "The analysis is not ready, please run denoising first". If I then go back to Denoising, click on Done, and select to skip already preprocessed seeds/subjects, then all the calculations are very fast as it probably just skips everything but then the 1st analysis is working.
Not sure if it can help, but I attach the log for this analysis (there is only one subject BTW).
Let me know if I can provide you with any additional helpful information, and thank you very much for taking the time to look into this issue,
Best regards,
Stephen