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help > RE: Native-space analysis with FreeSurfer segment
Nov 26, 2015 07:11 PM | Alfonso Nieto-Castanon - Boston University
RE: Native-space analysis with FreeSurfer segment
Hi Athena,
Some thoughts on your questions below
Best
Alfonso
Originally posted by Athena Demertzi:
Yes, if you prefer to use the FreeSurfer generated masks and have already entered those in Setup.ROIs then simply remove the segmentation step from the preprocessing list so those FreeSurfer-generated masks are not replaced by the SPM-generated masks.
2. When doing so, why my functional data are of different dimension compared to the T1,mgz and the segmented images?
The functional data is coregistered (but not resampled) to the structural volumes, so they will be in the same space (both in subject-space) but not necessarily having the same voxel dimensions. You may check that whether the structural and functional data is appropriately coregistered by going to the Setup.Functional tab and selecting 'functional tools. Check functional/anatomical coregistration'
3. Conn does not automatically load the art_outliers_and_movement file for the scrubbing 1st level covariate, is that normal?
CONN should be automatically loading, separately, the art_outliers file into a first-level covariate called 'scrubbing', and the estimated subject-movement parameters into a first-level covariated named 'realignment'. If it is not doing so check that a) the ARToutlier identification step was included as part of the preprocessing steps; and b) that the procedure terminated without any error messages
Hope this helps
Alfonso
Some thoughts on your questions below
Best
Alfonso
Originally posted by Athena Demertzi:
Thank you, Alfonso.
Can I ask you some more questions:
1. When using the proprocessing surface-based (single subject) pipeline, I need to remove the segmentation part, correct?
Can I ask you some more questions:
1. When using the proprocessing surface-based (single subject) pipeline, I need to remove the segmentation part, correct?
Yes, if you prefer to use the FreeSurfer generated masks and have already entered those in Setup.ROIs then simply remove the segmentation step from the preprocessing list so those FreeSurfer-generated masks are not replaced by the SPM-generated masks.
2. When doing so, why my functional data are of different dimension compared to the T1,mgz and the segmented images?
The functional data is coregistered (but not resampled) to the structural volumes, so they will be in the same space (both in subject-space) but not necessarily having the same voxel dimensions. You may check that whether the structural and functional data is appropriately coregistered by going to the Setup.Functional tab and selecting 'functional tools. Check functional/anatomical coregistration'
3. Conn does not automatically load the art_outliers_and_movement file for the scrubbing 1st level covariate, is that normal?
CONN should be automatically loading, separately, the art_outliers file into a first-level covariate called 'scrubbing', and the estimated subject-movement parameters into a first-level covariated named 'realignment'. If it is not doing so check that a) the ARToutlier identification step was included as part of the preprocessing steps; and b) that the procedure terminated without any error messages
Hope this helps
Alfonso
Threaded View
| Title | Author | Date |
|---|---|---|
| Athena Demertzi | Nov 24, 2015 | |
| Alfonso Nieto-Castanon | Nov 25, 2015 | |
| Alex G | May 26, 2022 | |
| derya | Oct 12, 2022 | |
| Athena Demertzi | Nov 26, 2015 | |
| Alfonso Nieto-Castanon | Nov 26, 2015 | |