Hello Josh,
When the randomise_parallel call has finished, you should have the “final” output files with filenames like: Analysis_Output_Name_corrp_tstat2.nii.gz along with the logs folder called Analysis_Output_Name_logs. The “final” critical value for the combined distributions is not explicitly output, but you could calculate it by taking a null distribution text file ( -N option), sorting it and then calculating the value at a given percentile.
Note that if you’re only interested in significant voxels, then the corrp images are all you need.
Hope this helps,
Kind Regards,
Matthew
> On 27 Jun 2016, at 17:03, Joshua Cruz <[log in to unmask]> wrote:
>
> Hi all,
>
> I'm relatively new to neuroimaging and running analyses with randomise. I used randomize_parallel to run my analysis and unlike running randomise without parallelizing, output files are put into a log folder. I'm running a comparative method analysis looking at clusters voxelwise, TFCE, cluster-size, cluster-mass.
>
> My question is for cluster-extent thresholding for size, where do I find the overall critical value associated with minimum cluster size? Each of the different seed files for my tstat of interest gives me similar but different numbers.
>
> For example, looking at the clusters_corrp_tstat2 critical values I get:
>
> SEED50
> ...
> Starting permutation 96
> Starting permutation 97
> Starting permutation 98
> Starting permutation 99
> Starting permutation 100
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED50_vox_corrp_tstat2 is: 5.49599
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED50_clustere_corrp_tstat2 is: 2581
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED50_clusterm_corrp_tstat2 is: 9485.82
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED50_tfce_corrp_tstat2 is: 34552.8
> Finished, exiting.
>
> or
>
> SEED46
> ...
> Starting permutation 96
> Starting permutation 97
> Starting permutation 98
> Starting permutation 99
> Starting permutation 100
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED46_vox_corrp_tstat2 is: 5.17889
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED46_clustere_corrp_tstat2 is: 2939
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED46_clusterm_corrp_tstat2 is: 10289.9
> Critical Value for: 2samplet_36n28_DBM_QwarpSS_SEED46_tfce_corrp_tstat2 is: 31906.8
> Finished, exiting.
>
> Here's the command i used:
>
> $ randomise_parallel -i Analysis_Name -o Analysis_Output_Name -d design.mat -t design.con -m Analysis_Mask.nii -n 5000 -D -T -x -c 2.9093 -C 2.9093 —uncorrp
>
> Thank you
>
> Josh
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