Try coping or linking the brain.mgz to brainmask.mgz
Robert Levy wrote:
Hi,
Yes, I set the rate to various values to test it, and all resulted in
the same threshold. I didn't mask to brain, because that causes an
error message (it cites the lack of a brainmap.mgz as the reason, so
that at least I know is due to it being processed in an older
stream). So I wonder if FDR requires that new processing as well, in
stable3. By the way, these are the commands I used for view the data:
setenv SUBJECTS_DIR /space/ventzl/1/users/SUBJECTS_DIR
source /usr/local/freesurfer/nmr-stable3-env
cd $SUBJECTS_DIR
tkmedit-sess -analysis EMerror -contrast ASevASc -space tal -map sig
-s BwGroupError5 -isxavg random -fthresh 1.3
Thanks,
Rob
Doug Greve wrote:
what do you mean by "staring p value"? Do you mean the FDR itself?
Robert Levy wrote:
Hi,
Is it possible to use FDR in stable3 for data that was processed
prior to the introduction of brainmask.mgz? It seems like I can
view the data just fine in stable3, or stable2 for that matter
(though not stable 4), but FDR gives results that seem wrong. FDR
sets the threshold to -log10(p)=4.279537 [p=.00005] no matter what
the starting pvalue is.
Thanks,
Rob
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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Fax: 617-726-7422
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