Hi Doug,
I analyzed my data using freesurfer 4.5, so I don't get the csdbase.sig.masked.mgh output.
Apart from re-analyzing my data using the up to date version of freesurfer, is there a way to get the csdbase.sig.masked output file using freesurfer 4.5?
Thanks for any suggestions.
Ben
Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262 ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, August 01, 2013 10:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] limiting display to significant clusters with tksurfer
Hi Ben, if you look at the help for mri_glmfit-sim (run with --help) it will detail the various outputs. one of them is csdbase.sig.masked.mgh which I think is what you want. best doug
On 8/1/13 9:09 PM, bbrent@bidmc.harvard.edu wrote:
Dear Freesurfers,
I ran a Monte Carlo analysis to identify significant clusters of activated voxels in a between-group comparison of fMRI data I've collected.
I was wondering if there was any way to limit what tksurfer displays to only the significant clusters based on the Monte Carlo -- i.e., those with a corrected cluster wise p < .05.
I know that you can display those clusters using the sig.cluster.mgh image file that is generated with the Monte Carlo analysis. But, the blobs in that map dont have any color variation and don't look the same way that activation does when typically using sig.nii (i.e., some are all yellow, orange or red).
Any help or suggestions would be much appreciated.
Thanks!
Ben Benjamin Brent, M.D., M.S. Massachusetts Mental Health Center 75 Fenwood Road, Room 618 Boston, MA 02115 617-754-1262
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
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.