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help > RE: Normalized structural files created, but not being displayed
Apr 18, 2022 09:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Normalized structural files created, but not being displayed
Hi Mary,
My guess is that at some point the structural data may have been manually switched to display the raw instead of the normalized images, but, assuming that this happened after the data had been already run through preprocessing, this would have had no effect on the results. In general the structural data is mainly used for estimating the Gray/White/CSF ROIs (this happens during preprocessing), and after that it is used only for display purposes, so I would probably suggest to check if the Gray/White/CSF ROIs appear to contain the correct (normalized) files, and if so then simply switch back your structural data in the Setup.structural tab to point to the normalized files so the subsequent displays use the proper information.
Best
Alfonso
Originally posted by Mary Newsome:
My guess is that at some point the structural data may have been manually switched to display the raw instead of the normalized images, but, assuming that this happened after the data had been already run through preprocessing, this would have had no effect on the results. In general the structural data is mainly used for estimating the Gray/White/CSF ROIs (this happens during preprocessing), and after that it is used only for display purposes, so I would probably suggest to check if the Gray/White/CSF ROIs appear to contain the correct (normalized) files, and if so then simply switch back your structural data in the Setup.structural tab to point to the normalized files so the subsequent displays use the proper information.
Best
Alfonso
Originally posted by Mary Newsome:
Hello Alfonso!
Recently I was going over a previous analysis and saw in the Setup that the functional data, GM/WM/CSF segmentations, and the ROIs were displayed as having been normalized (with 91x109x91), and I was surprised to see that the structural data did not display as having been normalized (displaying as the unprocessed data that had been entered), although all of the normalized structural files had been created and are in the subjects' directories. The unnormalized structural is also displayed in the 1st-level tab.
I am worried about how to interpret this. Since the fMRI displays as normalized, and the structural normalized files were created, is it possible that the normalized structural files had been used in the analysis and the activation is accurate, but just being overlaid onto a unnormalized structural image?
This was in an older analysis and was done in 16b. We have other analyses from around this time in the same version that do show the normalized structural.
As always, thanks for any help!
Mary
Recently I was going over a previous analysis and saw in the Setup that the functional data, GM/WM/CSF segmentations, and the ROIs were displayed as having been normalized (with 91x109x91), and I was surprised to see that the structural data did not display as having been normalized (displaying as the unprocessed data that had been entered), although all of the normalized structural files had been created and are in the subjects' directories. The unnormalized structural is also displayed in the 1st-level tab.
I am worried about how to interpret this. Since the fMRI displays as normalized, and the structural normalized files were created, is it possible that the normalized structural files had been used in the analysis and the activation is accurate, but just being overlaid onto a unnormalized structural image?
This was in an older analysis and was done in 16b. We have other analyses from around this time in the same version that do show the normalized structural.
As always, thanks for any help!
Mary
Threaded View
| Title | Author | Date |
|---|---|---|
| Mary Newsome | Apr 7, 2022 | |
| Alfonso Nieto-Castanon | Apr 18, 2022 | |