Segmentation error in Osprey batch processing

MRS Software Osprey
1

Dear all,

First, many thanks for developping Osprey, it is of such great help!

I am currently processing some data from an MRS study we conducted. However, I seem to get an error, while batchprocessing using the commandline in Matlab:

Segmenting structural image from dataset 9 out of 26 total datasets…
Arrays have incompatible sizes for this operation.

Error in OspreySeg (line 318)
GM_voxmask_vol = GMvol.private.dat(:,:,:slight_smile: .* vol_mask.private.dat(:,:,:);

Error in RunOspreyJob (line 45)
MRSCont = OspreySeg(MRSCont);

Related documentation

Strangely, this segmentation error only happend when running it via the command line. If i use the GUI it works perfectly fine. Does anyone on this forum perhaps know how to resolve this issue?

Additionally, how can I continue a job after an error? Now it continues with a new job and overwrites the existing job.

I hope someone can help!

Max

2

Hi @maxgrin,

Thank you for reaching out and happy to hear that you enjoy using Osprey.

My suspicion with this error is that somehow, the mask and the underlying segmentation files are mixed between subjects. Are you running the same jobfile once in the command line and once with the GUI?

It depends a bit on the error. If you can fix the error in the code. You can load the MRS container .mat file from the derivatives folder. It will contain the results from the previous analysis step. Then, you can rerun the step that failed. If you want to remove subjects that resulted in an error from the jobfile, you must rerun from the beginning.

Best,
Helge