Hi Doug,
Thanks for your help. A followup question to your last email: the short
term fix that you mentioned earlier, do I need to make that fix in addition
to copying the new mri_surfcluster file in the binary dir? Or has that been
fixed already?
Thanks,
Devdutta
On Mon, Mar 9, 2009 at 4:41 PM
Try copying this:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
into your $FREESURFER_HOME/bin directory (make a backup first), and then
re-run.
doug
Devdutta W wrote:
We are using Red Hat Enterprise Linux 5.
Thanks for your help. I'll try that out.
On Mon
We are using Red Hat Enterprise Linux 5.
Thanks for your help. I'll try that out.
On Mon, Mar 9, 2009 at 3:02 PM, Douglas N Greve
wrote:
> I think I've found the problem in that the original annotation at a vertex
> is not being cleared if a cluster is not there.
>
> The short term fix is to del
I think I've found the problem in that the original annotation at a
vertex is not being cleared if a cluster is not there.
The short term fix is to delete " --annot aparc" from mri_glmfit-sim at
line 353. I'll email when I have a longer term fix. What platform are
you using?
doug
Devdutta W
When I load mc-z.abs.2.sig.cluster.mgh, if the "Draw filled labels" button
is toggled on, it looks no different from before. Toggling the "show
overlay" button doesn't do anything.
If the "Draw Outlined labels" button is toggled on, the outlines of the
colored regions can be seen (including the ou
/what does it look like when you load mc-z.abs.2.sig.cluster.mgh as an overlay?/
Devdutta W wrote:
Nick, Sita,
The average subject is created from our data, perhaps that's why it
looks different. We were having problems getting freesurfer to
recognize our average subject. So we linked fsav
Nick, Sita,
The average subject is created from our data, perhaps that's why it looks
different. We were having problems getting freesurfer to recognize our
average subject. So we linked fsaverage to our average subject. I didn't
see a button (or a tool) to toggle on-off the annotation. The ove
Devdutta,
What version of freesurfer is being used? The fsaverage subject you
show doesnt look right. Also, I see what appear to be clusters mixed in
with the annotations. The summary files output by the multiple
correction step will tell you how many and the size of the clusters.
You should be
Hi Nick,
Can you shed some light on why this might be happening? I will attach the
two picture again in case you weren't able to view them last time. I tried
what I thought you meant by "turn off annotation display" and I have stated
what happened in my previous email (please see below)
- *If
Nick,
I confess, I am not exactly sure what you mean by "turn off annotation
display". I tried a few things.
- If I don't include the -annot option in tksurfer it only displays the
fsaverage, naturally.
- If I toggle off the button that says "show labels", it looks like it is
just
What is displayed if you turn off the annotation display?
The threshold in the simulation is used to determine whether clusters
are found or not. A threshold of 2 indicates a p-value of 0.01
(1/(10^2), 3 is 0.001, etc. The threshold referred to in the tksurfer
display is just for color threshold
11 matches
Mail list logo
