Jenifer,
The line is stddev (of the mean line in the plot).
Nick
On Wed, 2009-02-18 at 12:05 -0600, Juranek, Jenifer wrote:
> Hi,
>
> I’m running fsv420 on RHEL4. Within the qdec module (v1.2) menu
> options, View, Graph the ROI à generates average +/- SD or SE?
>
>
>
> Many Thanks,
>
> J
Jared,
Try adding the flag -ns 1 to your mri_convert command.
Nick
On Wed, 2009-02-18 at 11:33 -0500, Jared Price wrote:
> Dear gurus,
> when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz
> seg_edited_axial.nii to reslice from coronal to axial space we are
> seeing some s
Thank you for your quick reply Doug. After looking, I think you are referring
to the mri_glmfit tool? Is this the webpage to look at first to get started
learning about how to do cortical thickness group analysis?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Thank you,
Je
All those clusters are pretty small, so it does not surprise me that
they are not sig. Your command-lines look ok. I don't think the results
will change with more iterations.
dogu
Burmicz, Ryzarda wrote:
Hello,
I have just run a number of permutation and mc-z on data that was
previousl
If this is just a thickness study, then you dont need fsfast. There are
examples/tutorials of this type of analysis in the wiki. Look through
that and see if you still have questions.
doug
Jeff Sadino wrote:
Hello,
I want to run group statistics on the cortical thickness for a study
with 3 g
Hello,
I want to run group statistics on the cortical thickness for a study with 3
groups, each with about 30 subjects. To do this, I need to create an average
cort thickness map for each group. We are interested in basic statistics, so
nothing too advanced. I am wondering what would be the
Dear FS Team,
I used mris_divide_parcellation to create a new parcelation with smaller
regions, but they result in different sizes. I would need to get smaller
cortical parcellated regions, but all of them with similar areas. How can I get
it? Could I decide the area size of each new parcellate
Hi, Douglas
I´m making changes in aseg.mgz and I need to know how is the comand to save
the changes in the new segmentation (in tkmedit: File - New segmentation, or
File - Save segmentation or if there is another comand in the menu to save the
changes).
Hi,
I'm running fsv420 on RHEL4. Within the qdec module (v1.2) menu options, View,
Graph the ROI --> generates average +/- SD or SE?
Many Thanks,
Jenifer
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Hi Rysia,
Your commands looks fine to me, and 5000 iterations is good enough to see
significant cluster.
You might want to try lowering your threshold to 1.3 (0.05 p value).
thanks
pratap
> Hello,
>
>
>
> I have just run a number of permutation and mc-z on data that was
> previously analysed us
Lars M. Rimol wrote:
Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas ("blobs") on the cortical surface that
are above sig. threshold. I'd like to get a list of the vertex numbers
for each of these significant areas, which do not correspond
Hello,
I have just run a number of permutation and mc-z on data that was previously
analysed using qdec. Unfortunately none of my clusters reach significance (in
some cases there are no clusters found at all) and I am unsure as to what I am
doing wrong. I am running freesurfer v4.1.0 on Cent
can you be more specific? What are you using to create the manual
segmentations?
Kelly Silva wrote:
Hello,
I´d like to know what´s the comand to save the new manual
segmentations of the subcortical structures.
Thanks, Kelly
--
Undoubtedly, your 001.mgz has larger voxels, and so there will be some
changes in seg volumes. A better way to do this is with mri_label2vol.
First, you'll need the right registration file. Get that with:
tkregister2 --mov 001.mgz --targ orig.mgz --regheader --reg reg.001.dat
--noedit
Now ru
Hi,
Try like this,
Click inside your blobs.
Then click on the Custom Fill botton and then select "upto functional
value below threshold". This will select the cluster above the given p
value (1.3 in our case). Then click "fill".
Then click file->label->save selected label
this should work.
pr
Hello,
I´d like to know what´s the comand to save the new manual segmentations of
the subcortical structures.
Thanks, Kelly
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Dear gurus,
when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz
seg_edited_axial.nii to reslice from coronal to axial space we are
seeing some significant volume changes in the segmentation. Anyone know
why or how to fix it.
Jared
__
Hi,
I've done a glm model fit comparing cortical thickness between two
groups, and have certain areas ("blobs") on the cortical surface that are
above sig. threshold. I'd like to get a list of the vertex numbers for each
of these significant areas, which do not correspond to the parcellations in
FS
Hi Mike,
we haven't looked at them a lot, but we have found them to be
biologically meaningful at least in one case that I can think of.
cheers,
Bruce
On Tue, 17
Feb 2009, Michael Harms wrote:
Here is a question related to this whole discussion (prompted by what
Darren wrote):
As a practi
It seems to me that vertex areas in the native subject space are not
meaningful. The orig surfaces should be uniformly tesselated; however,
topology correction and final surface finding should introduce complicated and
probably uninteresting variation.
But, if a subject's surfaces are resampl
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