Dear Freesurfer team,
I have a manuscript under review which has used Freesurfer to compare
cortical thickness differences between groups, controls and patients with a
specific genetic mutation. There are robust, statistically
significant group differences in biologically plausible regions. Howeve
Dear FreeSurfer Experts,
I write in regard to the posting on calculating GM measures on a lobar basis.
I had a couple of quick questions:
1) Having derived a lobesfile using mri_annotation2label --subject
--hemi lh --lobesStrict lobesfile
one uses
mris_anatomical_stats -mgz -cortex ../labe
Dear Experts,
I apologise for the repost but I was wondering if anyone could guide me with
respect to deriving lobar measures and whether the commands below are correct .
Thanks. M
GM Lobar Values
(1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile
(2) mri_anatomica
Dear Experts,
I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean
ages that are not significantly different, though ranges/median are. I want to
compare cortical thickness between groups while allowing for age (age as
nuisance factor) but also want to see if there is a
Dear Doug,
Many thanks for reply. Given the age-group interaction, and the fact that even
when age is demeaned it simply means a difference in thickness will be tested
for at age=mean age (as opposed to age=0) can I at least interpret the findings
when using DODS model with age as a nuisance
Dear Experts,
I am trying to "back-normalise" significant clusters identified in a qdec
analysis (2 groups, thickness as main variable of interest) back into
individual subjects so that I can derive cortical statisitcs.
As per previous posts I have been trying to use mri_cor2label but am
running
Dear Doug,
Thanks for quick reply. Does it make a difference if I use mri_label2label
instead of mri_surf2surf for label propagation after I have used mri_cor2label
? Thanks.
M
On 5 Nov 2012, at 03:08, Mahinda Yogarajah wrote:
> Dear Experts,
>
> I am trying to "
Dear Experts,
Given that volume is area x thickness, how would one explain significant
reductions in volume in a qdec anaysis comparing patients and controls, but
not significant differences in area or thickness in the same regions where
volume differences are seen. All analyses use the same para
Hi,
Thanks for the reply. I am using the new script and I should correct myself in
that my significant volume changes do seem to correspond (although they are not
completely identical) to areas where there are significant area differences (I
see no significant thickness differences between my
Dear Experts,
I have a two groups - a control group and patient group. The patient group can
also be divided into 4 subgroups (but not control gp). Both groups are evenly
split between male and female. So far I have compared the patient and control
groups as a whole (age and icv as continuous/
Hi Donald and Doug,
Thanks for advice. Can I be a little bit clearer as I suspect I need a little
more guidance.
When comparing controls (gp c) and whole patient group (gp p) I see interesting
differences in area (DOSS model after checking for no interaction and with age
and ICV as correction
Hi Doug and Donald,
Again many thanks for the advice. With regard to the analysis described
previously - I have n=21 in my control group while P1=4 patients, P2=7
patients, P3=3 patients and P4=5 patients. Given that i have small numbers I
elected to compare only 2 patient groups (p1 and p4) r
Hi,
Thanks for the reference and explanation of the subtle statistical inferences.
It was very useful.
You are right in what i am trying to show (c- controls, p1 to p4 patients with
varying levels of endogenous factor) which is that when patients are subdivided
into levels of endogenous facto
Hi Doug,
Sorry the previous suggestion referred to a suggestion from Donald earlier in
the thread as follows:
"You might consider the contrast
[0 1.5 .5 -.5 -1.5] across all 5 groups showing a linear effect of
disease severity. The first column being controls."
I will try that suggestion out,
Hi,
I think (hope) i am finally getting to grips with how to analyse things but
wanted to check one last thing.
Say I have 1 factor with 3 levels (3 groups of subjects) and 2 covariates (age
and icv).
My design matrix would include:
Regressor 1 - ones for subject in Gp 1, 0 otherwise, codes
Hi - thanks - I was thinking about doing it the other way (3 separate groups)
because as well as looking to see whether there is a linear change in dependent
measures (eg area) across groups I also want to see if there is a linear change
in the slope of dependent measure against age across the
Hi - sorry probably being slow - not sure i follow - treating them as one group
(with appropriate covariate scale for level of endogenous factor/severity of
disease) and using scaled age scores how would i look for an interaction
between age and severity of disease across the group as both are
Dear Experts,
What references can I use in a write up for the use of area measures in both
vertex wise GLM and ROI based analyses. I have looked at the recommended
citation blurb on the website but see nothing about specific references for
area.
I am using FS v5.1 with the modified mris_ p
Hi,
Sorry to be a little more specific - I am aware of freesurfer area references
such as the WInkler reference but basically wanted a few lines, and the most
appropriate references, that summarises the technical approach used for group
area comparisons in qdec (using updated mris_preproc), an
borders of thalamus, pallidum, etc The brain*.mgz are
> for cortex, where we don't care about those borders.
>
> cheers
> Bruce
>
> On Thu, 24 Nov 2011, Mahinda Yogarajah wrote:
>
> Dear Experts,
>>
>> I am a beginner to the use of Freesurfer and having jus
Dear Freesurfer Experts,
I am processing some coronally acquired 3T GE FSPGR T1 volumes. I have
noticed that on occasion slices pial and white surfaces at the very front
of the brain can go very wrong - either frontal slices are excluded all
together (present in brainmask.mgz but no pial or wm su
Dear Freesurfer Experts,
I have read the advice on the wiki regarding what to do when pial surfaces
extend into the cerebellum. I had a few questions to clairfy things:
1) If I have made other (non-cerebellar) edits to the brainmask.mgz, and
added control points can I simply do
cp brainmask.mgz
Apologies for the repost - this may have got lost in the mail blackout ...
Dear Freesurfer Experts,
I have read the advice on the wiki regarding what to do when pial surfaces
extend into the cerebellum. I had a few questions to clairfy things:
1) If I have made other (non-cerebellar) edits to t
Dear Freesurfer Experts,
This might be a very basic question, and sorry for posting again, but I
would be grateful for any advice.
I have read the advice on the wiki regarding what to do when pial surfaces
extend into the cerebellum. I had a few questions to clairfy things:
1) If I have made ot
Dear Experts,
Sorry if this is a repost, but I was not sure it got posted.
I have a few subjects that I want to salvage and use where there appears to
be significant signal inhomogeniety in the last few frontal slices (see
T1.mgz in attached figure 1). Despite the use of control points (placed
w
it a slab selective acquisition and is anterior/posterior the
> slab direction?
>
> cheers
> Bruce
>
>
>
> On Mon, 23 Jan 2012, Mahinda Yogarajah wrote:
>
> Dear Experts,
>>
>> Sorry if this is a repost, but I was not sure it got posted.
>>
>>
t have coil coverage. I would try putting a line of control points in
> the white matter going from anterior and moving posteriorly until the
> drop-off is not that big (i.e. until the T1.mgz has voxels==110 in the
> white matter)
>
>
> On Tue, 24 Jan 2012, Mahinda Yogarajah wrote:
>
Dear Freesurfer Experts,
Would it be easier to upload a typical example of the data I am trying to
salvage, in order to get some hints on how I might proceed with this
problem of loss of frontal signal drop off ?
Thanks in advance.
Mahinda
On Thu, Feb 23, 2012 at 2:06 AM, Mahinda Yogarajah
Dear Experts,
I am trying to carry out a simple 2 group (conrol and patient) analysis
with ICV as nuisance factor, and thickness as the dependent variable.
However whenever I include ICV (inputed by following the qdec tutorial and
the generate stats table) I get the following output and error mes
the stddev).
> doug
>
> Mahinda Yogarajah wrote:
>
>> Dear Experts,
>>
>> I am trying to carry out a simple 2 group (conrol and patient) analysis
>> with ICV as nuisance factor, and thickness as the dependent variable.
>>
>> However whenever I inc
Dear Experts,
I wonder whether someone could explain to me how the monte-carlo correction
in qdec manages to be instantaneous. I appreciate it uses pre-computed
data, but I am a little confused. I thought that this sort of permutation
based method is based on relabelling of one's own specific dat
Dear Experts,
I had 2 questions with regard to vertex wise analysis using qdec.
1) How should one interpret the dependent variables area/pial area and
volume when comparing 2 groups with qdec and a vertex wise (as opposed to
ROI based) analysis - or are they uninterpretable in this context ? I re
TalY TalZ NVtxs Annotation
- --- -- - - --
1 -2.2596 47851.87 -22.0 -29.5 52.2 2195 precentral
2 -1.3197 24584.30 -38.1 50.0 -3.4 942
rostralmiddlefrontal
====
O
.
Mahinda
On Thu, May 3, 2012 at 5:47 PM, Douglas N Greve
wrote:
>
>
> On 05/01/2012 09:02 PM, Mahinda Yogarajah wrote:
>
>> Hi Doug,
>>
>> Thanks for the swift answer to the earlier questions - can I clairfy some
>> things:
>>
>> 1) Am I safe to use
Dear All,
Could someone explain (or point me in the right direction) as to the
meaning of the dependent measures (which can be used in qdec)
- intensity_deep/intensity_superficial
- intensity_deep.mgz/intensity_superficial.mgz
- white K/H
What do they represent ?
Thanks.
Mahinda
__
Dear Experts,
I have some related questions:
1) Am I right in thinking that the default settings for recon-all produce
aparc files where the areas are based on white matter and not pia ?
2) Therefore am I right in assuming that when I use aparcstats2table across
my subjects using "--meas area", t
qdec
...
6) An additional question - I note in the recon-all.log file that
mris_anatomical_stats is run with the flags "-mgz -cortex ... - what are
these flags for ?
Thanks.
Mahinda
On Mon, May 21, 2012 at 8:03 PM, Mahinda Yogarajah wrote:
> Dear Experts,
>
> I have some related qu
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