Hi
The messages are from a progress monitor. All it does is that for every given period of time, it checks the results folder and looks for output images of bedpostx. As parallelisation on a cluster happens on a slice-by-slice basis, it effectively checks how many slices have been processed. Depending on the time it takes for every slice to process and the computing resources, you can get different messages (e.g. Scenario 1 and 3). I.e. in Scenario 1, it does not skip slices, all it means is that between the two checks of the monitor two slices have been processed.
Scenario 2 can sometimes signal that something may have gone wrong with processing a slice. You can check your results, by making sure that all files mentioned in the online documentation have been produced and that they have the same number of slices as the input data.
Our experience is that the bedpostx monitor can cause a lot of confusion to users, so we will consider removing it in the next release.
Cheers
Stam
On 11 Feb 2014, at 16:26, Rodrigo Perea <[log in to unmask]> wrote:
> Dear fsl experts,
> I am trying to understand what happens with my bedpostx runs. For some reason I get different output in the command line but same number of files/folder (see below for each scenario). Anyway, here are my questions:
>
> 1. Why do I get different outputs command lines for different image but the same folder/files created.
> 2. How can I check whether my bedpostx run was successful or not (e.g. my 2nd run).
> 3. Should it be ok to skip the number of slices processed as in scenario 2 and 3).
>
> Thanks,
>
>
>
>
> Scenario 1.
> .
> .
> .
> 62 slices processed
> 64 slices processed
> 66 slices processed
> 69 slices processed
> Queuing post processing stage
>
>
> //The output in the *.bedpostX directory:
> $ ls -1 ../.xxxbedpostX/
> bvals
> bvecs
> commands.txt
> dyads1_dispersion.nii.gz
> dyads1.nii.gz
> dyads2_dispersion.nii.gz
> dyads2.nii.gz
> dyads2_thr0.05.nii.gz
> logs
> mean_dsamples.nii.gz
> mean_f1samples.nii.gz
> mean_f2samples.nii.gz
> mean_fsumsamples.nii.gz
> mean_ph1samples.nii.gz
> mean_ph2samples.nii.gz
> mean_S0samples.nii.gz
> mean_th1samples.nii.gz
> mean_th2samples.nii.gz
> merged_f1samples.nii.gz
> merged_f2samples.nii.gz
> merged_ph1samples.nii.gz
> merged_ph2samples.nii.gz
> merged_th1samples.nii.gz
> merged_th2samples.nii.gz
> monitor
> nodif_brain_mask.nii.gz
> xfms
>
>
>
> Scenario 2.
> .
> .
> .66 slices processed
> 67 slices processed
> 69 slices processed
> 71 slices processed
> Queuing post processing stage
> 75 slices processed
> For some reason the bedpostX process DOES NOT appear
> to have successfully completed. Please examine your
> results carefully.
>
>
>
> //The output in the *.bedpostX directory:
> $ ls -1 ../xxy.bedpostX/
> bvals
> bvecs
> commands.txt
> dyads1_dispersion.nii.gz
> dyads1.nii.gz
> dyads2_dispersion.nii.gz
> dyads2.nii.gz
> dyads2_thr0.05.nii.gz
> logs
> mean_dsamples.nii.gz
> mean_f1samples.nii.gz
> mean_f2samples.nii.gz
> mean_fsumsamples.nii.gz
> mean_ph1samples.nii.gz
> mean_ph2samples.nii.gz
> mean_S0samples.nii.gz
> mean_th1samples.nii.gz
> mean_th2samples.nii.gz
> merged_f1samples.nii.gz
> merged_f2samples.nii.gz
> merged_ph1samples.nii.gz
> merged_ph2samples.nii.gz
> merged_th1samples.nii.gz
> merged_th2samples.nii.gz
> monitor
> nodif_brain_mask.nii.gz
> xfms
>
>
> Scenario 3.
> .
> .
> .
> 61 slices processed
> 62 slices processed
> 63 slices processed
> 64 slices processed
> 66 slices processed
> Queuing post processing stage
> 75 slices processed
> All slices processed
>
>
>
> //The output in the *.bedpostX directory:
> $ ls -1 ../xxz.bedpostX/
> bvals
> bvecs
> commands.txt
> dyads1_dispersion.nii.gz
> dyads1.nii.gz
> dyads2_dispersion.nii.gz
> dyads2.nii.gz
> dyads2_thr0.05.nii.gz
> logs
> mean_dsamples.nii.gz
> mean_f1samples.nii.gz
> mean_f2samples.nii.gz
> mean_fsumsamples.nii.gz
> mean_ph1samples.nii.gz
> mean_ph2samples.nii.gz
> mean_S0samples.nii.gz
> mean_th1samples.nii.gz
> mean_th2samples.nii.gz
> merged_f1samples.nii.gz
> merged_f2samples.nii.gz
> merged_ph1samples.nii.gz
> merged_ph2samples.nii.gz
> merged_th1samples.nii.gz
> merged_th2samples.nii.gz
> monitor
> nodif_brain_mask.nii.gz
> xfms
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