Hi, In the mri_glmfit-sim command, when it does a "clusterwise correction" is it correcting across the whole brain? In other words, does the term "clusterwise" mean that it is only correcting within that cluster or is it correcting across the whole brain, cluster-by-cluster (instead of, say, voxel-by-voxel)?
While doing this analysis, (after displaying the .annot file in tksurfer as stated in the documentation), I noticed that our display did not match what was shown in the docs. In the documentation, the picture we are supposed to see only displays the clusters (all clusters, regardless of the significance). Ours displayed cortical parcellations in addition to the clusters. This may just be a display issue and the analysis might still be correct, but I just want to be sure. Has anyone else encountered this?
Thanks for any light anyone can shed on these questions.
Devdutta
It is for the whole brain. Not sure what you display command is, but mri_surfcluster will save all clusters in the cwp map. You can then set the tksurfer threshold to exclude the ones below your target sig level.
doug
Devdutta W wrote:
Hi, In the mri_glmfit-sim command, when it does a "clusterwise correction" is it correcting across the whole brain? In other words, does the term "clusterwise" mean that it is only correcting within that cluster or is it correcting across the whole brain, cluster-by-cluster (instead of, say, voxel-by-voxel)?
While doing this analysis, (after displaying the .annot file in tksurfer as stated in the documentation), I noticed that our display did not match what was shown in the docs. In the documentation, the picture we are supposed to see only displays the clusters (all clusters, regardless of the significance). Ours displayed cortical parcellations in addition to the clusters. This may just be a display issue and the analysis might still be correct, but I just want to be sure. Has anyone else encountered this?
Thanks for any light anyone can shed on these questions.
Devdutta
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your help. As regards to the display, I am using the command that is found in the mri_glmfit-sim documentation. Even with that command I don't see the display as it is shown in the documentation. In addition to showing the clusters (all of them), the display also shows what looks like cortical parcellations. I would just like to know why our picture isn't matching what is shown in the documentation even when we are following the docu. steps. If an attached picture will help, please let me know and I can attach one.
Thanks, Devdutta
On 2/24/09, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
It is for the whole brain. Not sure what you display command is, but mri_surfcluster will save all clusters in the cwp map. You can then set the tksurfer threshold to exclude the ones below your target sig level.
doug
Devdutta W wrote:
Hi, In the mri_glmfit-sim command, when it does a "clusterwise correction" is it correcting across the whole brain? In other words, does the term "clusterwise" mean that it is only correcting within that cluster or is it correcting across the whole brain, cluster-by-cluster (instead of, say, voxel-by-voxel)?
While doing this analysis, (after displaying the .annot file in tksurfer as stated in the documentation), I noticed that our display did not match what was shown in the docs. In the documentation, the picture we are supposed to see only displays the clusters (all clusters, regardless of the significance). Ours displayed cortical parcellations in addition to the clusters. This may just be a display issue and the analysis might still be correct, but I just want to be sure. Has anyone else encountered this?
Thanks for any light anyone can shed on these questions.
Devdutta
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Devdutta W -
Douglas N Greve