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help > RE: Export mask
Feb 19, 2021 01:02 AM | Alfonso Nieto-Castanon - Boston University
RE: Export mask
Hi Nick,
It is possible but it requires a bit of manual work, I would probably suggest something along the lines of:
1) use 'export mask' to create a "results.nii" mask with all of the individual clusters in your 2nd-level results
2) identify the ID's of each atlas region that you are interested in (e.g. by reading the contents of the conn/rois/atlas.txt file)
3) manually create each combined ROI using spm_imcalc. For example, to create an ROI that intersects your results cluster #2 with atlas region #57 (Precuneus) you could use something like:
spm_imcalc( {'results.ROIs.nii', '/software/conn/rois/atlas.nii'}, 'MyROI_Cluster2Precuneus.nii', 'i1==2 & i2==57');
Hope this helps
Alfonso
Originally posted by Nick Bray:
It is possible but it requires a bit of manual work, I would probably suggest something along the lines of:
1) use 'export mask' to create a "results.nii" mask with all of the individual clusters in your 2nd-level results
2) identify the ID's of each atlas region that you are interested in (e.g. by reading the contents of the conn/rois/atlas.txt file)
3) manually create each combined ROI using spm_imcalc. For example, to create an ROI that intersects your results cluster #2 with atlas region #57 (Precuneus) you could use something like:
spm_imcalc( {'results.ROIs.nii', '/software/conn/rois/atlas.nii'}, 'MyROI_Cluster2Precuneus.nii', 'i1==2 & i2==57');
Hope this helps
Alfonso
Originally posted by Nick Bray:
Hi
Alfonso,
I am also wondering if this is possible?
For context, I have completed a seed-voxel analysis using the right hippocampus as my seed. Two clusters have been identified as significant but one is largely (>50%) covering an unlabelled area of the Harvard-Oxford atlas. Therefore, I would like to export the clusters individually.
Cheers,
Nick
Originally posted by Tamir Eisenstein:
I am also wondering if this is possible?
For context, I have completed a seed-voxel analysis using the right hippocampus as my seed. Two clusters have been identified as significant but one is largely (>50%) covering an unlabelled area of the Harvard-Oxford atlas. Therefore, I would like to export the clusters individually.
Cheers,
Nick
Originally posted by Tamir Eisenstein:
Hi Alfonso and all CONN experts,
In the Results Explorer window under the clusters list there is a list of the corresponding areas from the Harvard-Oxford atlas for each identified cluster in the analysis.
Is there a way to export/create masks of these specific "sub-cluster" areas? For example, if I have a significant cluster which is composed of 250 voxels in the precuneus and 150 in the PCC, is there a way to export/create two seperate masks of these precuneus and PCC clusters?
Thanks!
Tamir
In the Results Explorer window under the clusters list there is a list of the corresponding areas from the Harvard-Oxford atlas for each identified cluster in the analysis.
Is there a way to export/create masks of these specific "sub-cluster" areas? For example, if I have a significant cluster which is composed of 250 voxels in the precuneus and 150 in the PCC, is there a way to export/create two seperate masks of these precuneus and PCC clusters?
Thanks!
Tamir
Threaded View
| Title | Author | Date |
|---|---|---|
| Tamir Eisenstein | Oct 4, 2020 | |
| Nick Bray | Feb 18, 2021 | |
| Alfonso Nieto-Castanon | Feb 19, 2021 | |
| Nick Bray | Feb 19, 2021 | |