Hi Doug,
I just got around to looking at this problem again and trying what you
had suggested (link brain.mgz to brainmask.mgz), and the problem is,
there is no brain.mgz either. I would expect to see it in
$SUBJECTS_DIR/$subject/mri/brain.mgz, but instead what I see, both in
individual subjects' mri directories, and in averaged brain mri
directories, does not include this file. Also, the COR files in
/space/ventzl/1/users/SUBJECTS_DIR/mano001/mri (for example), in the T1
volume, are dated 2003. I think the absence of brain.mgz indicates that
they were generated in a stream that was prior to not only brainmask.mgz
but prior to brain.mgz as well. I could not find release notes dating
that far back, but it seems like a reasonable assumption. Is it
correct? I can tell from the more recent release notes that COR files
were used in stable2 but no longer in stable3.
Not being able to apply the Mask to Brain option is certainly caused by
there not being files that would need to come from the newer recon-all
stream. Would you expect this to also cause FDR to not work? Is there
any way around this problem, given that there is no brain.mgz either?
Thanks much,
Rob
[vantz:mri] (nmr-dev-env) echo $SUBJECTS_DIR/
Doug Greve wrote:
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
--
Robert P. Levy, B.A.
Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2611
Charlestown, MA 02129
email: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
