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