Hello,
I generated a source grid in Brainstorm (March 6th 2019 version) in order to have the same size source grid for every subject. The individual subject's volume head model was generated using that source grid. I computed the sources using dSPM. Now, I'm trying to project those sources to the default anatomy. Currently, I'm getting this error when trying to project onto default anatomy:
Any suggestions?
There was a missing error message in the code, corresponding maybe to your problem. I fixed this is in this commit: https://github.com/brainstorm-tools/brainstorm3/commit/53cd00def999463783d3427aad086455bdb10e03
If you update Brainstorm, you would now probably get the following error message: 'You should compute the MNI transformation for the source MRI first.'
Display the MRI of your subject and click on "Click here to compute MNI transformation" and see if it fixes your problem.
Hello,
Thanks for the help. It worked for some of the subjects but following the same steps leads to different output file sizes in a few of the subjects. We can see that the functional data is not aligned when opening the NIFTI files in Freeview (functional data not the same size so we can see more voxels in one file compared to the other). Any ideas on what could cause this issue?
Thanks,
Butheina
Are you using the process "Export to SPM8/SPM12" process to export the volumes that are reprojected back to the MNI space? (you need this extra step after computing the sources)
If so, make sure you didn't select the option "cut the empty slices".
Hi,
Thank you again, your suggestion led to the brains being aligned, but even though the output file sizes are the same, the actual sizes look different in Freeview. Do we have to project onto the default anatomy before projecting onto the source grid?
Generate a common source grid for all your subjects, compute sources, and project the maps back to the template space. This is described in this tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects#Volume_source_models
I appreciate your help. I made the source grid as described in the tutorial and projected the maps back into the template space but they appear to be different sizes when exporting as Nifties. I described this issue earlier in the thread. I'm trying to figure out how to make sure that all my subjects are in the same space and are all the same size (or why they are not exporting to as Nifites this way). Do you have any suggestions for that?
Thanks,
Butheina
I'm not sure I understand what you mean: what is not the same size as what?
If you project all the sources back to the default anatomy, they are all available in the same volume (MNI ICBM152). If you export the all with the SAME OPTIONS (disable options "Cut empty slices", set the "Volume downsample factor" to 1, use the same time points) you should obtain volumes of the same sizes.
If you think there is a reproducible bug somewhere, please be more descriptive of the issue: describe step by step what you are doing, illustrating it with screen captures, and describe why you consider what you get is not the result you expect.
