Matlab toolbox for brucker extraction

functional-neuroimaging / rsfMRI-preprocessing

Use this code to preprocess and denoise your resting state fMRI time-series. Marco

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Matlab toolbox for brucker extraction #1

Open andyh742 opened 2 years ago

andyh742 commented 2 years ago

Hi,

From preprocessing I have resulted in upside down images (see below). I'm not sure why yet. Silvia thinks Vanja also had a similar issue and is trying to trace down what she did. However, I wanted to make others aware for future users.

We initially thought it was related to the "NIfTI_20140122" toolbox, but replacing that doesnt seem to have helped yet.

andyh742 commented 2 years ago

I didn't comment on this as I wasn't sure what the actual fix was. However @cmontani tells me she is having the same issue.

for me the thing that seemed to fix it was using a version of the NIfTI_20140122 toolbox which was hosted on the lab shared drive (link below). This is also what appeared to fix the issue for Vanja when she had the same issue. However, we couldnt figure out why as @silvia-gini found that the two packages were identical.

https://istitutoitalianotecnologia-my.sharepoint.com/:f:/r/personal/alessandro_gozzi_iit_it/Documents/FUNC_NIMAGING_LAB_RES/Procedures/scanner/import_scans/version_2015_07_10/dependencies?csf=1&web=1&e=EoDG1x

cmontani commented 2 years ago

2 things that could maybe fix this problem -in case of multi-user ws, the path for the NIfTI_20140122 toolbox must be inside your partition -add the MATLAB path in line 89 of the script "rsfmri_preprocess_00_extract_from_bruker.sh"

silvia-gini commented 1 year ago

Hi all, as you all know, we came across this same problem across multiple workstations. To add to what @cmontani has suggested, please make sure that when adding the path to MATLAB, you are pointing to version 2019b. This so far has solved things but we might want to look into a more stable solution.

lauramoutonhottier commented 7 months ago

Hi,

Where do you find NIfTI_20140122 toolbox ? I have bruker2nifti but there is no more dependency called NIfTI_20140122. Thanks,