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Hello Matthew,
I am using SLURM.
Through toggling around some parameters, I found the problem was with the automatic outlier deweighting. With that option turned on SLURM doesn't handle things properly. Any suggestions for altering the fsl_sub to fix this would be greatly appreciated.
Best,
Alexandra

On Fri, Nov 20, 2015 at 6:23 PM, Matthew Webster <[log in to unmask]> wrote:
Hello,
           Are you running this in some kind of parallel environment (e.g. a compute cluster )? A number of slices have not completed, which can be due to a cluster queue timeout.
Kind Regards
Matthew

> Dear Experts,
> I using FEAT to analyze data from subjects with multiple runs. Everything is fine on the 2nd level and a cope*.nii.gz is created for each subject. For my Group level, I entered those cope*.nii.gz files as inputs. And then something strange happens.
> I get this error
> /daten/share/opt/fsl/fsl-5.0.8-cscor/bin/smoothest -d 16 -m mask -r stats/res4d > stats/smoothness
> Mask and Data (residuals/zstat) volumes MUST be the same size!
>
> When I check res4d it has 49 slices.
>
> It seems to be originating from above:
> /daten/share/opt/fsl/fsl-5.0.8-cscor/bin/fslmerge -z stats0000/res4d.nii.gz stats0000/res4d stats0001/res4d stats0002/res4d stats0003/res4d stats0004/res4d stats0005/res4d stats0006/res4d stats0007/res4d stats0008/res4d stats0009/res4d stats0010/res4d stats0011/res4d stats0012/res4d stats0013/res4d stats0014/res4d stats0015/res4d stats0016/res4d stats0059/res4d stats0060/res4d stats0061/res4d stats0062/res4d stats0063/res4d stats0064/res4d stats0065/res4d stats0066/res4d stats0067/res4d stats0068/res4d stats0069/res4d stats0070/res4d stats0071/res4d stats0072/res4d stats0073/res4d stats0074/res4d stats0075/res4d stats0076/res4d stats0077/res4d stats0078/res4d stats0079/res4d stats0080/res4d stats0081/res4d stats0082/res4d stats0083/res4d stats0084/res4d stats0085/res4d stats0086/res4d stats0087/res4d stats0088/res4d stats0089/res4d stats0090/res4d
>
>
> Where it's creating a file with 49 slices instead of 91.
>
> Further up in the log I see this message for many of my slices (but not necessarily the ones that are missing):
> WARNING: The passed in varcope file, tmpvarcope0032, contains voxels inside the mask with zero (or negative) values. These voxels will be excluded from the analysis.
>
>
> The input copes all have 91 slices. Anyone know where this could be originating from? As part of FEATS clean up it seems to delete some of the files it would be useful at looking at to determine the problem.
> Any help would be greatly appreciated.
> Best,
> Alexandra



--
Alexandra DiFeliceantonio, PhD
Post Doctoral Fellow, Max-Planck-Institute for Metabolism Research
Visiting Post Doctoral Fellow, John B Pierce Laboratory at Yale University
+49 221 4726631
+1 203 562 9901 ext 209
"It would be surprising indeed if the brain were organized into spatially discrete units that conform to our abstract conceptualizations of behavior" Eliot Valenstein