what version of FS are you using? What is your bbregister command line? You should not smooth the data before alignment (usually you would use the template used for MC). You should also make sure that the deobliquing does not mess up the geometry info in the nifti file. Load the template file into freeview and make sure that it is aligned properly. Definitely do not convert it into MNI space.
On 1/26/18 5:50 PM, Rachel Bencic wrote:
Dear Freesurfer Team,
I am an image processing novice and am trying to register resting-state data to an anatomical scan using bbregister. The T1s have been run through Freesurfer's reconall pipeline, and the EPIs have undergone the following preprocessing steps:
- slice time correctoin
- deobliquing
- drop first few images
- motion correction / volume registration
- despike
- temporal filter
- smoothing
(I tried registering EPIs that had been aligned to MNI space to the anatomicals, with similar outcomes.)
Ultimately, I plan to use Freesurfer-generated ROIs (those from Yeo et al., 2011), based on the anatomical scan, to run graph theory analyses on the resting-state data.
However, when I use bbregister, the files are grossly misaligned. Below is an image of the EPI file on top of the white matter surface (in green). You can see that the EPI file looks very large.
Has anyone encountered this problem / does anyone have any suggestions as to what I might be doing wrong? Any help would be greatly appreciated.
Thank you in advance for your time.
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