help
help > RE: Structural/functional image overlay error
Jul 30, 2015 04:07 PM | Alfonso Nieto-Castanon - Boston University
RE: Structural/functional image overlay error
Hi Morgan,
That typically indicates a problem with the functional/anatomical coregistration and/or normalization. I would suggest to go to Setup.Functional and select there functional tools -> check coregistration of functional/anatomical files to see if those are appropriately coregistered. That will display the functional/anatomical data for the selected subject(s). If that shows an incorrect coregistration then the problem would be in your preprocessing steps (if you can give me more details about how your functional/anatomical data was originally preprocessed perhaps that will help figure out what might have gone wrong). If that display shows correct coregistration, then go to Setup.ROIs, select there one MNI-space ROI (e.g. the default "atlas" ROI) and select the ROI tools -> check coregistration option. That will display the coregistration between the MNI-space atlas and your structural file. If that display shows incorrect coregistration then the problem might be in the normalization part of your preprocessing steps (again in that case please give me more details about what those steps were to see if I can help). Last, if both of those displays look fine, then the only remaining potential issue would be to check in Setup.Options the selected 'analysis mask' option entered. If you have used an alternative 'explicit mask' (other than the default MNI-space mask) then again make sure that this mask is also appropriately coregistered to the functional data (in your case since all of the data is expected to be in MNI space I would probably suggest to leave this option in the default 'explicit mask' option which points to the mask.volume.brainmask file in the conn/utils/surf/ folder).
Let me know if any of these seems to be the issue here.
Best
Alfonso
Originally posted by Morgan Foreman:
That typically indicates a problem with the functional/anatomical coregistration and/or normalization. I would suggest to go to Setup.Functional and select there functional tools -> check coregistration of functional/anatomical files to see if those are appropriately coregistered. That will display the functional/anatomical data for the selected subject(s). If that shows an incorrect coregistration then the problem would be in your preprocessing steps (if you can give me more details about how your functional/anatomical data was originally preprocessed perhaps that will help figure out what might have gone wrong). If that display shows correct coregistration, then go to Setup.ROIs, select there one MNI-space ROI (e.g. the default "atlas" ROI) and select the ROI tools -> check coregistration option. That will display the coregistration between the MNI-space atlas and your structural file. If that display shows incorrect coregistration then the problem might be in the normalization part of your preprocessing steps (again in that case please give me more details about what those steps were to see if I can help). Last, if both of those displays look fine, then the only remaining potential issue would be to check in Setup.Options the selected 'analysis mask' option entered. If you have used an alternative 'explicit mask' (other than the default MNI-space mask) then again make sure that this mask is also appropriately coregistered to the functional data (in your case since all of the data is expected to be in MNI space I would probably suggest to leave this option in the default 'explicit mask' option which points to the mask.volume.brainmask file in the conn/utils/surf/ folder).
Let me know if any of these seems to be the issue here.
Best
Alfonso
Originally posted by Morgan Foreman:
Hi experts,
I am having trouble in the Conn toolbox when I get to the Denoising stage. All processing in Setup goes fine (no errors) but when I get to Denoising, the 'Preview effect of Denoising' image shows that the functional and structural images for my subjects aren't correctly overlapped (see attached image; this happens for ALL of the subjects). In Setup, the structural images I am using are normalized bias-corrected T1 images (wm) and my functional images are smoothed and normalized (sw). I can't find any issues with the Experiment Conditions or any other settings I have input. Any ideas on why this functional/structural overlay is so wrong?
Thank you,
Morgan
I am having trouble in the Conn toolbox when I get to the Denoising stage. All processing in Setup goes fine (no errors) but when I get to Denoising, the 'Preview effect of Denoising' image shows that the functional and structural images for my subjects aren't correctly overlapped (see attached image; this happens for ALL of the subjects). In Setup, the structural images I am using are normalized bias-corrected T1 images (wm) and my functional images are smoothed and normalized (sw). I can't find any issues with the Experiment Conditions or any other settings I have input. Any ideas on why this functional/structural overlay is so wrong?
Thank you,
Morgan
Threaded View
| Title | Author | Date |
|---|---|---|
| Morgan Foreman | Jul 29, 2015 | |
| Alfonso Nieto-Castanon | Jul 30, 2015 | |
| Morgan Foreman | Jul 30, 2015 | |
| Alfonso Nieto-Castanon | Jul 30, 2015 | |
| gol mi | Sep 9, 2017 | |