you can find it here fsaverage/surf/?h.white.avg.area.mgh
On 09/12/2016 11:26 AM, Claudia Dacquino claudia.dacqu...@gmail.com
[martinos-tech] wrote:
> Thanks Doug!
> Yes, I realized I was wrong and I wrote to the freesurfer list too.
> Just another question,as you were so prompt in
Hi Claudia, it is better to post these things to the freesurfer list as
martinos-tech is no longer active. The total cortical surface area
(65416.6mm2) is incorrect. The total should be 82219.960938. The
reported value is the actual surface area of the fsaverage white
surface. However, the
you would create a mask from the uncorrected results, eg,
mri_binarize --i condAvfix.sig.mgh --min 2 --o condAvfix.sig.mask.mgh
mri_binarize --i condBvfix.sig.mgh --min 2 --o condBvfix.sig.mask.mgh
fscalc condAvfix.sig.mask.mgh and condBvfix.sig.mask.mgh - o
condA-and-Bvfix.sig.mask.mgh
The
Hi Doug,
Thanks. Just to confirm, for the negative-only maps, I assume I would set
max = -2 in mni_binarize, e.g.:
mri_binarize --i condAvfix.sig.mgh --max -2 --o condAvfix.sig.neg.mask.mgh
mri_binarize --i condBvfix.sig.mgh --max -2 --o condBvfix.sig.neg.mask.mgh
Is that correct?
~Sue
On
correct
On 12/04/2013 01:40 PM, Susan Ruiz wrote:
Hi Doug,
Thanks. Just to confirm, for the negative-only maps, I assume I would
set max = -2 in mni_binarize, e.g.:
mri_binarize --i condAvfix.sig.mgh --max -2 --o condAvfix.sig.neg.mask.mgh
mri_binarize --i condBvfix.sig.mgh --max -2 --o
Hi Doug,
I have been running this analysis as I described in my previous email by
clustering pos and neg activation separately using glmfit-sim for
condAvfix, condBvfix, and condAvcondB, and then making conjunction maps. It
occurred to me that you had mentioned in your response that is might be
Hi Doug,
That makes total sense! Thanks so much for looking into this.
Best,
Suzanne
On Tue, Oct 29, 2013 at 3:57 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
For condition 4 (posslope), the weight is always 0. You can't compute a
slope if all the values are the same.
doug
On
I mean to take all the values (eg, .68849, .31061, etc), compute their
mean, then subtract the mean from each value. This will not affect the
slope calculation but can affect the offset. Seeing differences in the
offsets does not mean that anything is fundamentally wrong.
doug
On 10/29/2013
Hi Sue, that looks correct. I think it is an open question as to whether
you should use the corrected maps or use the uncorrected and then
correct the final map. Maybe someone else can chime in.
doug
On 10/23/2013 09:49 AM, Susan Ruiz wrote:
Hi Doug,
This is /very/ helpful.
Hi Suzanne, why would you not just re-run mri_glmfit-sim with the
different vertex wise threshold? If you want to use 20 voxels, then
you'd have to look a the table and see what cluster p-value that
corresponds to with vertex threshold = .005
doug
On 9/11/13 10:20 AM, Suzanne Oosterwijk
Hi Doug,
Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like to
do is to apply a more liberal threshold to my data to examine the clusters
that fall outside of the MC-corrected threshold. To do this I applied the
mri_surfcluster command with a vertex-wise threshold of p .005,
Suzanne,
p0.005 is the same whether its voxels or vertices.
The liberal nature of 20 voxels is vague to begin with as there is two
things contributing to how liberal 20 voxels are: (1) voxel size - 20 1mm
isotropic voxels is quite different from 20 3mm isotropic voxels; (2) The
number of voxels
Hi Suzanne, I'll cc the FS list so others can benefit ...
On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote:
Hi Doug,
I have two follow-up questions to enhance my own understanding of
Freesurfer. I know that MC simulations take into account the
smoothness of the data. I noticed that the
Not sure. In principle no, but it might cause the brain to be
non-centered or out of the field of view. I would just run tkregister2
--fstal --s subject and get it more-or-less right (or at least check
that it is not out of the field of view).
doug
On 06/12/2012 09:32 AM, Yue, Xiaomin wrote:
Hi Doug,
Thank you for your quick response!
At the moment I have 8 data sets that are ready to be preprocessed. I am
still running my experiment in the scanner though, so by the end of the
summer I should have around 22 data sets. At the moment recon2 is running
on 7 data sets for which I have
Hi Suzanne, it does not mean that there is anything wrong with your
data. I've seen this before on some data sets. I have a work-around that
might work. How many data sets do you have to run?
doug
On 05/29/2012 02:35 PM, suzanne oosterwijk wrote:
Hi,
Recently I ran recon1 for several
Hi Aly,
you can load multiple overlays in tksurfer either on the command line or
from the GUI. The same is true of freeview.
cheers,
Bruce
On Sat, 6 Nov 2010, Aly Negreira wrote:
Hi All,
I'm sure this is ridiculously simple, but cant seem to load two
sig.mgh files (both are cortical
so doug we ran them using qdec. can you expand?
On Tue, Oct 13, 2009 at 6:00 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
It depends on which program you ran and how you ran it.
Frida Polli wrote:
hey bruce, nick, doug
when we use qdec to generate simulations to find CWP,
It depends on which program you ran and how you ran it.
Frida Polli wrote:
hey bruce, nick, doug
when we use qdec to generate simulations to find CWP, the cluster
sizes that we get are smaller area than if we make a label from the
cluster and use label_area to determine the size of the
I am re-sending an email that Doug wrote earlier this week, as it was a
thorough description of some pretty important changes to the average
subject and talairach subject.
There is a new average subject to replace average7 that ALSO replaces the
talairach subject. It is called fsaverage and
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