Dear FreeSurfer experts,
I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons.
My question is about how do I correctly get the FDR corrected results showing cluster number, size, MNI coordinates etc. as I would if I used QDEC?
I have searched through the archives and have found what looks like the answer, but I'm not convinced that the method I used is correct.
I used
1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs --cwpvalthresh .99
and
2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary
However when I visualize the FDR corrected results with tksurfer or freeview I can see a couple of clusters not listed in the summary. Am I missing something?
Thank you so much in advance.
Any help or advice would be greatly appreciated.
Best wishes
Marco
You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr to the FDR you want. Set --subject fsaverage and set the ---hemi. Set --annot aparc. Set --sum to the output summary file. This should give you something similar to the output of mri_glmfit-sim.
On 6/29/17 4:29 PM, marco mcsweeney wrote:
Dear FreeSurfer experts,
I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons.
My question is about how do I correctly get the FDR corrected results showing cluster number, size, MNI coordinates etc. as I would if I used QDEC?
I have searched through the archives and have found what looks like the answer, but I'm not convinced that the method I used is correct.
I used
- mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs
--cwpvalthresh .99
and
- less
lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary
However when I visualize the FDR corrected results with tksurfer or freeview I can see a couple of clusters not listed in the summary. Am I missing something?
Thank you so much in advance.
Any help or advice would be greatly appreciated.
Best wishes
Marco
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
thank you so much for the feedback and all of your help!
Best wishes
Marco
On Thu, Jul 6, 2017 at 1:45 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You can use mri_surfcluster. Set the sig.mgh as the --in file. Set --fdr to the FDR you want. Set --subject fsaverage and set the ---hemi. Set --annot aparc. Set --sum to the output summary file. This should give you something similar to the output of mri_glmfit-sim.
On 6/29/17 4:29 PM, marco mcsweeney wrote:
Dear FreeSurfer experts,
I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons.
My question is about how do I correctly get the FDR corrected results showing cluster number, size, MNI coordinates etc. as I would if I used QDEC?
I have searched through the archives and have found what looks like the answer, but I'm not convinced that the method I used is correct.
I used
- mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs
--cwpvalthresh .99
and
- less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.
cluster.summary
However when I visualize the FDR corrected results with tksurfer or freeview I can see a couple of clusters not listed in the summary. Am I missing something?
Thank you so much in advance.
Any help or advice would be greatly appreciated.
Best wishes
Marco
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas Greve -
marco mcsweeney