Hi John
I do not know anything about the error that you are getting but I was also having some problems with tksurfer and was told by Dr. Fischl that this viewer is no longer being updated and that it would be best to try freeview. Did you give this a go?
best wishes
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Mar 16, 2016 at 9:43 AM, John Anderson j.anderson@publicist.com wrote:
Dear experts, I am running into a trouble visualizing my data in tksurfer. I highly appreciate any advice that can help! I ran group analysis between two groups using GLM analysis (mri_glmfit) and I corrected the results for multiple comparison using (mri_glmfit-sim), then I ran this command to visualize the results:
tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh
The result attached. In my summary file I see that I have significant differnce only in the precentral gyrus. But the results in tksurger is not showing precentral gyrus. I tried to play with the thresholds and nothing changed.
Any advice is highly appreciated!! Bests, John
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it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI
On 3/16/16 9:43 AM, John Anderson wrote:
Dear experts, I am running into a trouble visualizing my data in tksurfer. I highly appreciate any advice that can help! I ran group analysis between two groups using GLM analysis (mri_glmfit) and I corrected the results for multiple comparison using (mri_glmfit-sim), then I ran this command to visualize the results: tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh The result attached. In my summary file I see that I have significant differnce only in the precentral gyrus. But the results in tksurger is not showing precentral gyrus. I tried to play with the thresholds and nothing changed. Any advice is highly appreciated!! Bests, John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Why do you say something is wrong? It is a big cluster and probably not very useful. Is that what you mean? If so, then increase the threshold.
On 3/16/16 10:44 AM, John Anderson wrote:
Thank you doug, Please what do you suggesst me to do? Is this related to something wrong in the analysis? Bests, John *Sent:* Wednesday, March 16, 2016 at 10:42 AM *From:* "Douglas Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI On 3/16/16 9:43 AM, John Anderson wrote:
Dear experts, I am running into a trouble visualizing my data in tksurfer. I highly appreciate any advice that can help! I ran group analysis between two groups using GLM analysis (mri_glmfit) and I corrected the results for multiple comparison using (mri_glmfit-sim), then I ran this command to visualize the results: tksurfer fsaverage lh inflated -overlay cache.th13.pos.sig.cluster.mgh The result attached. In my summary file I see that I have significant differnce only in the precentral gyrus. But the results in tksurger is not showing precentral gyrus. I tried to play with the thresholds and nothing changed. Any advice is highly appreciated!! Bests, John _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
John Anderson -
Trisanna Sprung-Much