Hi,
I have a problem with make_average_subject.
After running all commands (including ln -s
$FREESURFER_HOME/subjects/fsaverage
and recon-all -s -qcache for all my subjects) about running QDEC, I
found that QDEC could not analysis my group.
Because the group have 1 factor and three level
Hi all,
I have 2 groups of subjects and I want to do a volume group analysis
to compare volumes of subcortical structures.
I have to run my analysis with the command-line methods but I don't
know the correct flags to
use with the commands (mris_preproc and mri_glmfit).
Can you help me? Can you
Hi,
I've used the fdr function in tksurfer and compared the results to Tom Nichol's
matlab function (http://www.sph.umich.edu/~nichols/FDR/). I use p =
10.^-abs(pfile), where "pfile" is 'sig.mgh'.
I find that the p-threshold (pID, assuming positive dependence) is usually
exactly the sam
To make analysis of volumetric data export volumetric data to csv and use your
statistical package.
-- Pedro Paulo Jr
E71 Nokia
-Msg original-
De: Anita di Iasio
Enviada: 25/06/2009 06:04:38
Para: freesurfer@nmr.mgh.harvard.edu
Assunto: [Freesurfer] volume group analysis
Hi all,
I h
Hi All,
After running the dt_recon processing stream on a standard diffusion
tensor image, does any body know the units on the resulting adc.nii
volume?
Thanks
Greg
--
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh
Hi,
Please disregard my previous mail. I was a little too trigger happy..., the
1.928 threshold set by tksurfer is too high for any vertex to survive so the
two methods DO concur. I should actually look at the maps and not just the
output...
The reason I asked is that I'm combining i
Use the fast_fdrthresh matlab function provided in the fsfast/toolbox directory
in freesurfer. It gives the same results as tksurfer.
Cheers
Jorge Luis Bernal Rusiel
Phd Student
Laboratory of Functional Neuroscience.
University of Pablo de Olavide. Seville. Spain
--- El jue, 25/6/09, Lars
Hi
I have four questions on label-design:
1.) Is there a way do design labels of a certain geometric form (e.g. a
circle or a square with a standardized diameter) in tksurfer ?
2.) Can I move an existing label from one positition to another defined
position (e.g. center it on some particular ver
1. Not really, although you can dilate a label, which will be somewhat
circular.
2. No, sorry.
3. You can save it and reload it as a new one I guess.
4. Not sure, I'll leave this one for Doug
Bruce
On Thu, 25
Jun 2009 adrze...@nmr.mgh.harvard.edu wrote:
Hi
I have four questions on labe
Feng-Xian,
It appears that you do not have permission on your system to change the
limits. So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out the 'limit'
line, so that it looks like this:
#limit descriptors unlimited
Nick
On
Feng-xian,
I should also mention that i dont think creating your own average
subject will solve the problem you describe, where you need to work with
three levels in your group. for that, you wont be able to use qdec, but
will need to run things manually. these pages give examples:
http://surfe
Anita,
to add to that comment, you would use asegstats2table to create the text
file of data of your subjects and their stats of volumetric data, which
can be imported into any stats package. see this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VolumetricGroupAnalysis
while its po
Mike (and Jorge),
Thanks!
yours,
LMR
> Subject: [Fwd: Re: [Freesurfer] setting of fdr thresholds in qdec]
> From: mha...@conte.wustl.edu
> To: freesurfer@nmr.mgh.harvard.edu; lari...@gmail.com
> Date: Thu, 25 Jun 2009 10:08:05 -0500
>
>
> Lars,
> I had a similar question regard
Yes, it will always give a value such that nothing is above threshold.
I'm not sure that the actual FDR threshold is defined in such cases.
doug
Lars M. Rimol wrote:
Hi,
Please disregard my previous mail. I was a little too trigger
happy..., the 1.928 threshold set by tksurfer is too high
It means that you have an ill-conditioned design matrix. It is probably
the case that your discrete or continuous variables are redundant or
that you don't have members in all your classes.
doug
Toh Hock Wong wrote:
Hi to all,
I have been having troubles with qdec and several error messages
Can you be more specific? I would not recommending pooling them together.
doug
Krishna Srihasam wrote:
Hi,
We had collected a lot of data in our first few scan sessions trying
different TR/TE/voxel size/REPs combinations in order to get the
optimal values. Now, I would like to do a joint ana
류철형 wrote:
>
> Dear all
>
> I'm trying to compare the cortical thickness between the
> neurodegenerative disease patient group and normal controls.
>
> To match the age, I selected subjects from both groups and finally
> included age-matched groups into freesurfer thickness analysis
> (similar me
The easiest thing would be to binarize the aparc+aseg like:
mri_binarize --i aparc+aseg.mgz --wm --o whitematter.mgz
You can the resample this to mni305 with:
mri_convert --apply_transform transforms/talairach.xfm whitematter.mgz
whitematter.mni305.mgz -oc 0 0 0
Not sure what you want to do
You will have to do it with the "command-line stream". Ie, set up your
own FSGD file with classes and covariates, run mris_preproc, create your
own contrasts, then run mri_glmfit. There are examples on the wiki.
doug
Feng-Xian wrote:
Hi,
I have a problem of group analysis with QDEC. Now, I w
You don't *have to* to run make_average_subject to do your analysis,
only if you want to view the results on a map with the curvature
patterns averaged over your subjects. As for the limit error, how old is
your version of freesurfer? That line was removed about 1.5 years ago...
doug
Feng-Xia
You can use mris_preproc or mri_glmfit. Instead, use asegstats2table.
This will create a text table that you can load into a stats program.
See the wiki tutorial for examples.
doug
Anita di Iasio wrote:
Hi all,
I have 2 groups of subjects and I want to do a volume group analysis
to compare v
They are the inverse of the units that you used to spec the b-values.
doug
Gregory Dierksen wrote:
Hi All,
After running the dt_recon processing stream on a standard diffusion
tensor image, does any body know the units on the resulting adc.nii
volume?
Thanks
Greg
--
Douglas N. Greve, P
#4. Not yet, though I have started working on this again, but it will be
a while before it is ready. Carl Schwartz gave a solution a while ago,
search the archives. It's not great, but you can do it now.
doug
Bruce Fischl wrote:
1. Not really, although you can dilate a label, which will be som
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