Closed cselenyi closed 4 years ago
VeraKer
commented
4 years ago Hi, this is great! Excited to try the 3D slicer! Regarding that, however, Matlab had trouble adding the slicer toolbox/setting the path because the folder \slicer\ did not exist. I created it and downloaded 3D slicer in it, which solved that.
However when choosing to inspect ROIdefs with 3D slicer the following error occurs:
@cselenyi What could the solution for that be?
cselenyi
commented
4 years ago @VeraKer OK, that's because the new little toolbox coupling Solena/MATLAB to 3D slicer is not on your MATLAB path. And it cannot be because I forgot to share that as an independent toolbox on ecat7_nfs! Both 3D slicer and this "slicer" toolbox is available from within Solena workers but in order for it to work also as an inspection tool (what you were wanting to try) both 3D slicer and the "slicer" toolbox needs to be installed into ecat7_nfs. I am doing that now. I see that you placed 3D slicer software into the ".../m-files/slicer" on ecat7_nfs but that's not the correct setup. That folder will host the "slicer" coupling toolbox. The program itself will be in another folder next to it called "Slicer-4.10.1-win-amd64", containing the Windows PC 64-bit version of 3D Slicer (note that version 4.10.2 is a later one but that has a bug, that's why we stick to version 4.10.1). For best loading performance for 3D slicer it is possible to install 3D Slicer (version 4.10.1) on your own PC. In that case the toolbox will launch your local copy (hopefully :-) ). You can actually find the installer package pre-downloaded into the "slicer" toolbox folder on ecat7_nfs: ../downloads/m-files/slicer/Slicer-4.10.1-win-amd64.exe. Good luck!
cselenyi
commented
4 years ago OK, now it's uploaded. Solena in theory should automatically add the "slicer" toolbox to the MATLAB path. To do it manually add: Y:\downloads\m-files\slicer (not sure of your drive letter but it's the ecat7_nfs share).
The new version accompanies the new release of the Solena Manager. It addresses several smaller issues and adds some new features:
Manual ROI delineation functionality: relies on the newly coupled Slicer 3D software to enable advanced ROI creation and editing (as well as inspection) functionality into Solena pipelines.
Blood curve assembly: "obtain_blood" is now able to take into account the time-delay and correction of early manual samples taken during the ABSS sampling period. This is not enabled by default, see help "solena_docFunction obtain_blood" as to how you can modify the layout to include this correction. To be used by caution (though it appears to improve match between ABSS and early manual samples..).
Improved SPM12 read/write. It turns out that SPM12 was using a sophisticated but unfortunately buggy Microsoft feature to access data (called file mapping), which could produce truncated PET image frames or empty (zero) slices in e.g. segmentation mask files for data processed on the network (which we all do since our data are on network shares). This was a nasty, unpredictable bug. I have modified SPM12 in the workers to use straightforward read/write operations which don't expose this issue. Please QC especially your segmentation results from before to see if there are zero planes (e.g. in _seg_grey _seg_white and _seg_brain) and also 4D PET images after realignment (less likely to have the issue though) or image calculation steps. Reprocess if necessary using the new worker.
Many others which I don't recall now.. :-)