Hi everyone,

so excited to use this amazing software and joing this community.

I'm using the last software version and I'm looking for a way to build up a preoprocessing pipeline on subject space and not in MNI space, using also the coregistration step.

When I figure out the result (on denoising step) there are always a mismatch between the structural and the functional brain images.

In attach the preprocessing pipelines I used I used and the brain mismatched images.

Any ideas?

Thank you

Alberto

1) 

• functional Label current functional files as "original data"


• functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)


• functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)


• structural Center to (0,0,0) coordinates (translation)


• functional Center to (0,0,0) coordinates (translation)


• functional Direct coregistration to structural (rigid body transformation)


• functional Outlier detection (ART-based identification of outlier scans for scrubbing)


• functional Segmentation (Grey/White/CSF segmentation)


• structural Segmentation (Grey/White/CSF tissue estimation)


• functional Smoothing (spatial convolution with Gaussian kernel)


• functional Label current functional files as "smoothed data”

2) 

• structural Center to (0,0,0) coordinates (translation)


• functional Center to (0,0,0) coordinates (translation)


• functional Direct coregistration to structural (rigid body transformation)


• functional Label current functional files as "original data"


• functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)


• functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)


• functional Outlier detection (ART-based identification of outlier scans for scrubbing)


• functional Segmentation (Grey/White/CSF segmentation)


• structural Segmentation (Grey/White/CSF tissue estimation)


• functional Smoothing (spatial convolution with Gaussian kernel)


• functional Label current functional files as "smoothed data”

3)

• structural Center to (0,0,0) coordinates (translation)


• structural Segmentation (Grey/White/CSF tissue estimation)


• functional Label current functional files as "original data"


• functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)


• functional Center to (0,0,0) coordinates (translation)


• functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)


• functional Direct coregistration to structural (rigid body transformation)


• functional Outlier detection (ART-based identification of outlier scans for scrubbing)


• functional Segmentation (Grey/White/CSF segmentation)


• functional Smoothing (spatial convolution with Gaussian kernel)


• functional Label current functional files as "smoothed data"