Dear all,
I have a few questions about stats in freesurfer that I'd be very grateful if you could answer.
1. Is it possible to reduce the search from the whole brain to a smaller region of interest to apply corrections for multiple comparisons? For example, if I'm interested in differences in the fusiform gyrus, can I restrict the FDR correction to the fusiform?
2. Is it important to control for any global measure when comparing cortical thickness? For example when comparing grey matter volume, it's good practice to control for the intracranial volume. In case of cortical thickness (and other dependent measures in freesurfer), do you know how these are affected by the intracranial volume (or other measures) and how these could be controlled?
3. Finally, I posted a question a few days ago about comparing volume using freesurfer. I'm sorry for insisting on this but I still haven't found any response. My question was whether it's possible to compare volume maps in freesurfer. I'm using an older version (4.0.4) and my impression is that the most recent version might have this feature, but this is unclear to me. I'd be very grateful if you could let me know if this is the case. And if there's any way in which I can compare volumes usig data pre-processed using the version I have.
Thank you very much!
Best wishes,
Lucia
Lúcia Garrido wrote:
Dear all,
I have a few questions about stats in freesurfer that I'd be very grateful if you could answer.
- Is it possible to reduce the search from the whole brain to a smaller
region of interest to apply corrections for multiple comparisons? For example, if I'm interested in differences in the fusiform gyrus, can I restrict the FDR correction to the fusiform?
Yes, click in the fusiform, click on the "Mark Label" button (or tools->Labels->Mark Selected Label), then check the "Only Marked" button next to the FDR, then "Set Threshold Using FDR", the "Apply".
Not sure about the others.
- Is it important to control for any global measure when comparing
cortical thickness? For example when comparing grey matter volume, it's good practice to control for the intracranial volume. In case of cortical thickness (and other dependent measures in freesurfer), do you know how these are affected by the intracranial volume (or other measures) and how these could be controlled?
- Finally, I posted a question a few days ago about comparing volume
using freesurfer. I'm sorry for insisting on this but I still haven't found any response. My question was whether it's possible to compare volume maps in freesurfer. I'm using an older version (4.0.4) and my impression is that the most recent version might have this feature, but this is unclear to me. I'd be very grateful if you could let me know if this is the case. And if there's any way in which I can compare volumes usig data pre-processed using the version I have.
Thank you very much!
Best wishes,
Lucia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Many thanks for your e-mail. I've tried to do what you suggested to correct with FDR just using specific regions, but i couldn't find the buttons you mentioned. I thought it was my qdec version so I downloaded the most recent version of freesurfer and did recon all <subject> qcache with everyone. But again I don't see the buttons you said on this version of qdec. Am I missing something terrribly obvious? Could it be that it doesn't work with data pre-processed with earlier version?
Many thanks for your help,
Lucia
Lúcia Garrido wrote:
Dear all,
I have a few questions about stats in freesurfer that I'd be very grateful if you could answer.
- Is it possible to reduce the search from the whole brain to a smaller
region of interest to apply corrections for multiple comparisons? For example, if I'm interested in differences in the fusiform gyrus, can I restrict the FDR correction to the fusiform?
Yes, click in the fusiform, click on the "Mark Label" button (or tools->Labels->Mark Selected Label), then check the "Only Marked" button next to the FDR, then "Set Threshold Using FDR", the "Apply".
Not sure about the others.
- Is it important to control for any global measure when comparing
cortical thickness? For example when comparing grey matter volume, it's good practice to control for the intracranial volume. In case of cortical thickness (and other dependent measures in freesurfer), do you know how these are affected by the intracranial volume (or other measures) and how these could be controlled?
- Finally, I posted a question a few days ago about comparing volume
using freesurfer. I'm sorry for insisting on this but I still haven't found any response. My question was whether it's possible to compare volume maps in freesurfer. I'm using an older version (4.0.4) and my impression is that the most recent version might have this feature, but this is unclear to me. I'd be very grateful if you could let me know if this is the case. And if there's any way in which I can compare volumes usig data pre-processed using the version I have.
Thank you very much!
Best wishes,
Lucia
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Lúcia Garrido