MRIDude

This morning I looked into this an little further. It is occurring because the sqlite file already exist. This has never happened to me before. However I have not run...

It has been some time since I posted this. I concluded that it was the upgrade to pypids 0.17.0. I remember it not being a version mismatch. I would have...

Here is the list of installed packages on conda [bidscondaenv.txt](https://github.com/user-attachments/files/15794050/bidscondaenv.txt) Though I have bids validator installed via conda. I realized to get it to show up on the command line...

Yes. It points to a binary in conda environment.

It is already in the path. In the fact, it is the very first folder in the path. However, I added it anyway, I got the same error.

OK, I tried that out. everything look good except it set the c_ras to zeros.

Ok here is the updated script ```python import nibabel as nb import numpy as np import sys oldfilledmgz = nb.freesurfer.mghformat.load(sys.argv[1]) newfilledmgz = nb.freesurfer.mghformat.load(sys.argv[2]) WMmgz = nb.freesurfer.mghformat.load(sys.argv[3]) oldfilled=np.asanyarray(oldfilledmgz.dataobj) newfilled=np.asanyarray(newfilledmgz.dataobj) WM=np.asanyarray(WMmgz.dataobj) if...

This does help. I ran the code again and used the output for it in FreeSurfer's recon-all and it fails. After some investigation i figured out that the output of...