I have seen this issue in one other post on this forum, but unfortunately it did not mention if a solution had been found. Whenever I try to load my own data (Siemens) into the Osprey GUI it errors on the load data step. I have tried it without the waterfile and/or T1 as well.
I am using a Siemens scanner and the data I have got from it is .IMA. It does take single averages and saves them seperately for the single voxel spectrum, but it also creates an average of these 80 files into one .IMA file.
I have attached the spectro, water, and T1 file, as well as my LogFile and matlab JobFile (test). I have tried CoReg via Gannet before, but it does not seem to register my voxels on the right spot. I have tried to play around with the rotations as mentioned in certain documentation, but whereas it does indeed rotate the position, it is still not close to the actual spot. My main goal is to obtain the tissue percentages within the voxels to correct for them during the quantification. When I saw Osprey also has a quantification step I hoped I would be able to use this as well, it seems like a great tool to exist in the world of spectroscopy.
The voxel position of attached data should be in the vermis (the thin middle part within the cerebellum) and I have placed the voxels on the obtained T1 scan (in sag/tra/cor dimensions) during scanning. If you have any ideas on how to adjust Osprey/Gannet to be able to read this data I would be very grateful!
Thanks for reaching out! I’ll take a look at the issue. Just a few quick questions:
- Is this unedited/conventional data?
- Do you have a reference image with the voxel position taken on the scanner?
Also, if you do have the single average DICOM files, I’d recommend you to use those instead of the scanner averaged files. If you do so, you’ll have to supply the path to the folder including all single average IMA files instead of the path to a single file.
Do you happen to have the original DICOM images from the T1 scan as well? I just want to check whether something happened during the DICOM to NifTI conversion.
I have made a .ima folder in the drive with the seperate IMA files (192) that I put into mricron to convert to NifTI.
I hope you are having/had a good holiday period I was wondering if you were able to find any explanation for the issue? I’ve been going through the script more closely now I’m back from vacation, but was not able to find a solution as of yet.
Have you tried using the most recent version? I’ve made some adaptions to the code that could possibly solve the problem (Voxel flipped L-R when using nifti T1 for GE data - #17 by mollysimmonite).
Or have you tried this already?
Hi @Helge ,
I have tried that now and GannetLoad and GannetFit do give me output, however whenever I want to include a .nii file it gives me an 'Unable to perform assignment because the size of the left side is 240-by-173 and the size of the right side is 240-by-173-by-3. I have tried my best troubleshooting and searching if the error has an easy fix, but I can’t seem to find a proper solution. Have you perhaps seen this before?
Thank you for your replies so far!
I’ve seen this error happen before (in Gannet). I’m not sure exactly why it happens, but try restarting MATLAB. This usually fixes it for me.