Hello,
What could be the reason to get bigger surface area from WM surface
than from the pial surface in the 3 labels?
Thank you!
Andreia
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Fri, 28 Mar 2014 17:43:43 +
De: _andre...@sapo.pt
Assunto: Re: [Freesurfer]
Hi Andreia,
which one is bigger? In your first email you said pial (which should be)
and in your second you said white matter
cheers
Bruce
On Sun, 30 Mar 2014,
_andre...@sapo.pt wrote:
Hello,
What could be the reason to get bigger surface area from WM surface
than from the pial surface
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The
values of the example are correct.
Thanks!
Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Andreia,
which one is bigger? In your first email you said pial (which should be)
and in your second you said white
Hello experts,
I'm working with FS 5.3.0. When I used 'mri_glmfit-sim --glmdir
/home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs
--cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got
an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a
Hi FS experts
I completed group analysis by this
method:http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons
. Now I want to represent the result just the way as non-surface(please see
attachment). I want to know how to load sig.mgh by
Hi FS experts
I have done the group thickness analysis(two group t-test), and get the
result(i.e. sig.mgh). I got one cluster in the sig.mgh file. I want to convert
this cluster into each subject specific original space(i.e brainmask.mgz).
Thanks.
All the best.
Rujing Zha
2014-03-30
and what do the surfaces look like in those regions? For the wm surface
are to be larger it probably needs to be a lot less smooth
On Sun, 30 Mar 2014, _andre...@sapo.pt wrote:
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The
values of the example are correct.
How do I overlay aparc labels in tkmedit? I can load Brodmann area
labels, but not aparc.
Thanks!
Andreia
Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what do the surfaces look like in those regions? For the wm surface
are to be larger it probably needs to be a lot less smooth
On
the easiest way is to just use the aparc+aseg.mgz
cheers
Bruce
On Sun, 30 Mar 2014,
_andre...@sapo.pt wrote:
How do I overlay aparc labels in tkmedit? I can load Brodmann area
labels, but not aparc.
Thanks!
Andreia
Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what do the
Dear FreeSurfer Experts,
I would like to extract the mean thickness for each subject, and I can see that
in the lh.aparc.stats, there are three lines. For example:
# Measure Cortex, NumVert, Number of Vertices, 107414, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4,
I cannot properly access my desktop PC today, tomorrow I'll give you
feedback, However, with a corase inspection the surfaces look ok.
Thank you Bruce!
Andreia
Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu:
the easiest way is to just use the aparc+aseg.mgz
cheers
Bruce
On Sun, 30
I think aparcstats2table automatically includes these measures. Can you
check? And, yes, mean thickness can be computed as (lh+rh)/2
doug
On 3/30/14 12:58 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I would like to extract the mean thickness for each subject, and I can
see that in the
I don't know what you mean by represent as non-surface. To load in
tksurfer run
tksurfer fsaverage lh inflated -aparc -overlay sig.mgh
On 3/30/14 11:16 AM, charujing123 wrote:
Hi FS experts
I completed group analysis by this
On 3/29/14 3:09 PM, Ashley Shurick wrote:
Hi,
I have some questions about using monte carlo sim in qdec:
First of all, I just want to verify it's ok to use the simulation with
a whole-brain analysis and not just an ROI analysis.
yes
Second, I'm a bit confused about how to calculate the
How did you create the glmdir? mri_glmfit should set things up so that
all of those files are there
On 3/30/14 11:09 AM, yd li wrote:
Hello experts,
I'm working with FS 5.3.0. When I used 'mri_glmfit-sim --glmdir
/home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs
I think I would just run mri_glmfit on your data to get the proper
directly structure and estimate of FWHM, then copy the sig file from the
mixed fx analysis into the glmfit folder for one of the contrasts. Then
run mri_glmfit-sim.
doug
On 3/29/14 10:29 AM, Pedro Rosa wrote:
Dear Doug
Thanks! Instead of aparcstats2table, I just used grep and awk to retrieve those
directly from the ?h.aparc.stats, and then I calculated the mean_thickness =
((lh_mean_thickness * lh_white_surface_area ) + (rh_mean_thickness *
rh_white_surface_area)) / (lh_white_surface_area +
I have a clarifying question about fsgd file format.
We have 40 participants, and a large battery of individual difference
measures (egg., vocabulary, phonological skill, etc.)
We applied a PCA to the battery and found 4 components, corresponding to
WMC, processing speed, comprehension ability,
I'm not sure I understand (sorry for being obtuse!) We don't want to check
for interactions among nuisance variables (inasmuch as we only have
the one, the average thickness). Rather, we want to check for interactions
among the four factors revealed by our PCA, controlling for the nuisance
Sorry, that should have been interaction among continuous (not
necessarily nuisance) variables. You will need to create new variables
that are products of your variables of interest in order to test for
interactions.
doug
On 3/30/14 9:20 PM, Clint Johns wrote:
I'm not sure I understand
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