Hello,
The log file is frozen at saving p-values. All the permutations have run and then I get:
...100% [Design 1/1, Contrast 2/2, Shuffling 5000/5000, Modality 1/1]
Elapsed time with permutations: ~ 20929.9 seconds.Computing p-values. Saving p-values (uncorrected, and corrected within modality and within contrast). =>> PBS: job killed: walltime 540037 exceeded limit 540000
I am running the analysis on the university supercomputer. I feel like it might be stuck on an error, but no error message has appeared on any of the runs I have tried. I keep raising the walltime, but even with 150 hours, PALM did not finish running. I can try running it using more processors per node, I just wanted to make sure that it makes sense for this to be talking so long.
Thank you,
Kelly
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Anderson M. Winkler <[log in to unmask]>
Sent: Monday, January 27, 2020 6:07 PM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] PALM issue saving p-valuesHi Kelly,
Either PALM is still running (it seems it is from your message) or it has crashed. These tstat files are saved at the beginning as they don't need permutations, but the p-values can only be produced at the far end.
If you don't have access to the console where it's running (say, because it's in a cluster and somehow you can see the log files), then you can check that it has finished successfully if the files results_1_21_2020_elapsed.csv have been produced.
Hope this helps!
All the best,
Anderson
Thank you Paul,
I tried specifying the -ise to run sign flipping. I was able to run PALM using the settings:-i /fs/project/hcppalm/task_01_13_2020/Cope10combinednew.dtseries.nii -transposedata-d /fs/project/hcppalm/task_01_13_2020/designmatrix.mat-t /fs/project/hcppalm/task_01_13_2020/C.con-eb EBnew.csv -ise-o /fs/project/hcppalm/task_1_21_2020-n 5000 -corrcon -logp -accel tail -nouncorrected
I have gotten a couple outputs:results_1_21_2020_dat_tstat_c1.dscalar.niiresults_1_21_2020_dat_tstat_c2.dscalar.nii
I believe I should be getting more outputs than this. According to the tutorial I should get a result with the p-values FWER and the p-values FWER across all contrasts from all designs, but PALM has been running for 150 hours (for ~700 subjects, 2 contrasts) and I have not gotten the p-value results.
Any ideas?
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Paul Zhutovsky <[log in to unmask]>
Sent: Monday, January 27, 2020 7:08 AM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] PALM issue saving p-valuesHi,
I think you want to run a sign-flipping test and not a permutation test. For this you would need to specify the '-ise' option in PALM. See this example.
Cheers,Paul
Hello,
I do have a column of just ones for my design matrix, which I thought was to represent the input COPE image, so the first four columns are information such as age, gender, education, etc. Then the fifth column is a column of ones for the COPE input image.
I have attached the my con matrix. I am not attaching the design, as it has restricted data, but I am attaching a sample with only 5 subjects. My actual design matrix is similar, only with over 700 subjects.
Thank for the help!
Kelly
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Colin Hawco <[log in to unmask]>
Sent: Monday, January 13, 2020 3:22 PM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] PALM issue saving p-valuesThe key things here, I think:
Generating 1 shufflings (permutations only).
For whatever reason PALM can only make 1 permutation. For example, you
gave it a column of 1's in the design matrix, and it is trying to run
shuffling instead of sign flipping.
Maybe paste in your design and con matricies.
Colin
Quoting Kelly Hiersche <[log in to unmask]>:
> I am having the same problem while running PALM. I get the following output:
>
> Running PALM alpha116 using MATLAB 9.7.0.1190202 (R2019b) with the
> following options:
> -i Cope10combinednew.dtseries.nii
> -transposedata
> -d designmatrix.mat
> -t C.con
> -eb EBnew.csv
> -o results
> -n 5000
> -corrcon
> -logp
> -accel tail
> -nouncorrected
> Found HCP Workbench executable in
> /usr/local/connectome-workbench/1.3.2/bin_rh_linux64/wb_command
> Reading input 1/1:
> /fs/project/PAS1418/hcppalm/motor_01_13_2020/Cope10combinednew.dtseries.nii
> Reading design matrix and contrasts.
> Elapsed time parsing inputs: ~ 7.05839 seconds.
> Number of possible permutations is 1.
> Generating 1 shufflings (permutations only).
> Building null distribution.
> 50% [Design 1/1, Contrast 1/2, Shuffling 1/1, Modality 1/1]
> Saving file: /fs/project/PAS1418/hcppalm/results_dat_tstat_c1
> Number of possible permutations is 1.
> Generating 1 shufflings (permutations only).
> Building null distribution.
> 100% [Design 1/1, Contrast 2/2, Shuffling 1/1, Modality 1/1]
> Saving file: results_dat_tstat_c2
> Elapsed time with permutations: ~ 10.6722 seconds.
> Computing p-values.
> Saving p-values (uncorrected, and corrected within modality and
> within contrast).
> { Unable to perform assignment because the size of the left side is
> 1-by-1 and
> the size of the right side is 0-by-1.
>
> Error in palm_competitive (line 96)
> S(infpos,c) = max(S(~infpos,c)) + 1;
>
> Error in palm_datapval (line 67)
> [~,cdfG,distp] = palm_competitive(Gvals(:),'descend',true);
>
> Error in palm_pareto (line 78)
> P = palm_datapval(G,Gdist,rev);
>
> Error in palm_saveall (line 246)
> Ptosave =
>
> palm_pareto(plm.G{y}{m}{c},plm.Gmax{y}{m}{c},false,opts.accel.tail_thr,opts.accel.G1out);
>
> Error in palm_core (line 2489)
> palm_saveall(plm,opts);
>
> Error in palm (line 81)
> palm_core(varargin{:});
> }
>
>
> I am working with the HCP data (restricted and unrestricted).
>
> Any suggestions/help would be appreciated!
>
> Thanks,
>
> Kelly
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1__;!!KGKeukY!n2unrmGioD_x7P_9DZb89w_FV7d3Eh9GywS7BueE-t7czu1VQAjbttPdAPOEC4B5$
########################################################################
To unsubscribe from the FSL list, click the following link:
https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1__;!!KGKeukY!n2unrmGioD_x7P_9DZb89w_FV7d3Eh9GywS7BueE-t7czu1VQAjbttPdAPOEC4B5$
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1