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help > RE: How to identify regions in ICA spatial components with atlas
Jan 24, 2022 11:01 PM | Alfonso Nieto-Castanon - Boston University
RE: How to identify regions in ICA spatial components with atlas
Hi,
Yes, you may use the function "conn_coords2label" to get the atlas-based region at some pre-defined MNI coordinate, e.g.
labels = conn_coords2label([10, -10, 0]);
to get the label at those coordinates using the default CONN atlas, or the syntax:
labels = conn_coords2label([10, -10, 0], '/myfolder/myatlas.nii');
to get the label at those coordinates using an alternative atlas.
That said, if I am understanding correctly, it may be simpler to just run a new second-level analysis that looks at one ICA spatial map and computes a one-sample t-test across all subjects (e.g. selecting AllSubjects and entering a between-subjects contrast 1), and then display those results using the results explorer in order to see where those clusters (which are going to represent what brain regions tend to be represented in those ICA spatial maps) are located
Hope this helps
Alfonso
Originally posted by sat2020:
Yes, you may use the function "conn_coords2label" to get the atlas-based region at some pre-defined MNI coordinate, e.g.
labels = conn_coords2label([10, -10, 0]);
to get the label at those coordinates using the default CONN atlas, or the syntax:
labels = conn_coords2label([10, -10, 0], '/myfolder/myatlas.nii');
to get the label at those coordinates using an alternative atlas.
That said, if I am understanding correctly, it may be simpler to just run a new second-level analysis that looks at one ICA spatial map and computes a one-sample t-test across all subjects (e.g. selecting AllSubjects and entering a between-subjects contrast 1), and then display those results using the results explorer in order to see where those clusters (which are going to represent what brain regions tend to be represented in those ICA spatial maps) are located
Hope this helps
Alfonso
Originally posted by sat2020:
Good afternoon,
I have thoroughly searched previous posts but cannot figure out how to do this. I ran a group ICA in Conn 20b and when displaying results for contrasts in the Results Explorer, was able to see for the significant regions, what the atlas-based regions of the significant clusters were and export that info to a table. I also have a specific atlas that I was able to load, and that worked perfectly in determining what regions are at the cluster. Unfortunately, I have not been able to get this atlas to load in either FSL or AFNI but it was very easy to do in Conn.
I am interested in summarizing what brain regions tend to be represented in the ICA spatial maps I chose for these group comparisons, and want to make sure I'm being consistent by using the same atlas. is there a way for me to get that information from Conn somehow, even if it were command-based in Matlab? Essentially, I would want to know for probably the center of gravity for each ICA spatial map (some of which have several "clusters" in the network), what are the atlas-based regions at that coordinate. Is there a way to do this?
Thanks for any assistance you can provide!
I have thoroughly searched previous posts but cannot figure out how to do this. I ran a group ICA in Conn 20b and when displaying results for contrasts in the Results Explorer, was able to see for the significant regions, what the atlas-based regions of the significant clusters were and export that info to a table. I also have a specific atlas that I was able to load, and that worked perfectly in determining what regions are at the cluster. Unfortunately, I have not been able to get this atlas to load in either FSL or AFNI but it was very easy to do in Conn.
I am interested in summarizing what brain regions tend to be represented in the ICA spatial maps I chose for these group comparisons, and want to make sure I'm being consistent by using the same atlas. is there a way for me to get that information from Conn somehow, even if it were command-based in Matlab? Essentially, I would want to know for probably the center of gravity for each ICA spatial map (some of which have several "clusters" in the network), what are the atlas-based regions at that coordinate. Is there a way to do this?
Thanks for any assistance you can provide!
Threaded View
| Title | Author | Date |
|---|---|---|
| sat2020 | Jan 23, 2022 | |
| Alfonso Nieto-Castanon | Jan 24, 2022 | |
| sat2020 | Jan 25, 2022 | |
| sat2020 | Feb 6, 2022 | |