I have been working with some students to run several HERMES data sets through Osprey, and we have found a few interesting wrinkles/bugs.
First one - when using the GUI to create a job file on my Mac (Macbook pro 2019, Quad-Core Intel Core i5, running Monterey. Using Matlab 2021b, and Osprey 2.3) for more than 1 file the job file created has extra spaces after tseveral of the file paths in the Job file list before closing the quotation marks. So for example:
“files”: ["/Path/To/Files/sub-01/ses-01/sub-01_ses-01_ROI-01_act.SDAT "
This also happens for the water reference files, but interestingly, not for the T1 anatomical image files.
I got around this by editing the jobfiles in Matlab, but thought you guys might want to be aware of it, incase others get the same problem.
Then my students had a different problem. One is running Osprey 2.3 in Matlab on a windows machine (I don’t know the specifics sorry, but it’s likely Matlab 2022a or 2022b as they just installed Matlab). When this student used the GUI to crete a job file, the file paths were created using “” instead of “/” for the file paths. So:
Editing the job file to the above (‘D/Path/To/…’) fixed the issue and the student could then use the job file to run the data using:
MRSCont = RunOspreyJob('OspreyJob.m)
Which ran all the way through fitting the data, segmenting etc (as seen by the results turing up in the output folder) but it gave an error
Error using mkdir
The filename, directory name, or volume label syntax is incorrect.
Error in OspreyHTMLReport (line 49)
Error in RunOspreyJob (line 58)
[MRSCont] = OspreyHTMLReport(MRSCont,kk);
and no MRSCont was made in the workspace. I’ll try to have a dig into the actual job file that was created to see if there is some hint there, but any advice or ideas appreciated.