Hi,
To which voxel space (native, Talairach or any other
standard space) do the measured cortical thickness
and areas/volumes in the statistical output files refer?
Ed
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
native
cheers,
Bruce
On Thu, 4 Jun 2009, Ed Gronenschild wrote:
Hi,
To which voxel space (native, Talairach or any other
standard space) do the measured cortical thickness
and areas/volumes in the statistical output files refer?
Ed
___
Freesurfer
It will be whatever you used as input. In this case, it is the -log10(p)
value of the maximum in the cluster (not the thickness value).
doug
Pratap Kunwar wrote:
Hi Judith,
Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster.
Hi all. After looking over our
Hi, experts,
I am interested in only the positive sulc and would like to make group
analysis of the postive sulc values. Hence I would like to mask off the
negative values (as the lh.sulc file has both positive and negative value).
Before making group analysis, I have to resample and smooth
Thanks, for you responses Doug and Pratap. But, both of your responses need
more clarification, because I believe that we are not all referring to the
same 'max'.
Doug:
I understand that when I display the sig.cluster.mgh that the a CWP value
of 0.0001 would be displayed as a 4 by the color
This is an annoyance with the way the summary stats are produced. When
we run the program that generates the stats table, we pass it
FreeSurferColorLUT.txt and ask it to report on all the segmentations in
the LUT. The problem is that no segmentation volume has *all* of these
individual
Doug,
Thanks for the reply. So when I see 0's, does this mean that a match
for that label does not exist in this brain? This would make sense
for hypointensities, but I am consistently getting 0's for the
internal capsule, which should exist in every brain.
Thanks,
Dana
At 01:01 PM
It might mean that it does not exist in that brain or in that
segmentation volume. Eg, aseg.mgz will not have any of the cortical
structures because they are not defined in aseg.mgz (but are in
aparc+aseg.mgz).
Dana W. Moore wrote:
Doug,
Thanks for the reply. So when I see 0's, does
The max is the -log10(p), bounded below by -log10(CWP) for positive
correlations Hence with an -log10(CWP) of 4, the Max
will be greater than 4, and will specify the maximum -log10(p) value in that
cluster, occuring at VtxMax
Is this right for -log10(p) kind if input? This is how i have been
It is the maximum vertex-wise -log10(p) found in the cluster. Why do you
think otherwise? You should be able to load the sig map into tksurfer
and go to that vertex to find out.
doug
Judith Segall wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses
need more
Zhangyuanchao wrote:
I would like to mask off the
negative values (as the lh.sulc file has both positive and negative
value).
Another way to filter the sulc is:
$mris_calc -o lh.sulc.pos lh.sulc gte 0
which filters 'lh.sulc' and only lets values that are greater than or
equal to 0
The Max is somewhat unrelated to the CWP. The Max is the vertex-wise
maximum and is bounded below by the vertex-wise threshold. The CWP
(cluster-wise p-value) which is derived from the size of the cluster,
the smoothness, and the size of the search space. It is not necessary
for the CWP to
Hi Dana,
there are a bunch of structures that we have labels for in the table, but
don't actually segment (yet!).
cheers,
Bruce
On Thu, 4 Jun 2009, Dana W. Moore wrote:
In my wmparc.stats file I have noticed that for many structures I am just
getting a value of 0. I do get output for ctx
Hi all,Just wondering if the scan orientation for input DICOMs matter.
I know that Analyze format does not preserve left/right orientation
information, but would a saggital DICOM scan have the same problem?
We have a lot of axial scans, would incorporating freesurfer subjects with
saggital scans
we will read it from the dicom and adjust for it accordingly
cheers
Bruce
On Thu, 4 Jun
2009, David Qixiang Chen wrote:
Hi all,Just wondering if the scan orientation for input DICOMs matter.
I know that Analyze format does not preserve left/right orientation
information, but would a saggital
The orientation itself does not matter in terms of running FS on an
individual. However, I would be very careful about doing a statistical
analysis where some subjects are axial and some are saggital as the
change in the phase encode direction can cause bias. At the very least,
any comparisons
Doug and freesufer list.
When I load the sig map in tksurfer i know that the CWP is displayed as the
-log(10)p; however, I am not asking about visualization or the CWP. The
newest version of the wiki does a great job in explaining the p values. I
am only asking about the sig.cluster.summary
Dear Freesurfers,
is it feasible to save to nii the MR images after stripping the skull in
Freesurfer? If so, please let me know how to do it.
Thanks in advance.
Best,
Jose
---
Jose Luis Cantero, Ph.D.
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cellular
The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you
load the FSGD and look at the scatter plot, the y-axis will be the
thickness value (assuming you're doing a thickness study:).
doug
Judith Segall wrote:
Doug and freesufer list.
When I load the sig map in tksurfer i
Doug.
Again, I am only asking about the sig.cluster.summary. This was a thickness
study, where monte-carlo simulations where used to correct for multiple
comparisons. Why would the *max in column 2 of the sig.cluster.summary* be
derived from the sig.mgh and not the sig.cluster.mgh? Since, this
The sig.mgh is the input that creates the sig.cluster.mgh (and the
summary table).
doug
On Thu, 4 Jun 2009, Judith Segall wrote:
Doug.
Again, I am only asking about the sig.cluster.summary. This was a thickness
study, where monte-carlo simulations where used to correct for multiple
just
mri_convert brainmask.mgz brainmask.nii
doug
On Thu, 4 Jun 2009, Jose Luis Cantero Lorente wrote:
Dear Freesurfers,
is it feasible to save to nii the MR images after stripping the skull in
Freesurfer? If so, please let me know how to do it.
Thanks in advance.
Best,
Jose
---
sure, just run mri_convert on the brainmask.mgz and give the output
volume the .nii extension
cheers
Bruce
On Thu, 4 Jun 2009, Jose Luis Cantero Lorente
wrote:
Dear Freesurfers,
is it feasible to save to nii the MR images after stripping the skull in
Freesurfer? If so, please let me know
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