Hello,
I am wondering if there is an easy way to determine the size of a cluster
of significant voxels resulting from a QDEC analysis? I have created a
label and mapped the label to all of the subjects, but didn't know if there
was a way to extract information about cluster size.
Thanks,
Mi
Hi,
I'm running Qdec to gather cortical thickness in specific regions based on
the scalar visuals.
when I've drawn ROIs over certain areas, I've found "Mapping labels to
subjects" would return an error message for certain subjects.
There error is as follows:
ERROR: srcvtxno = -1 < 0
trgvtxno = 11
Sorry for the confusion. Let me rephase my questions.
question 1: I want to use the example_func2highres.mat created by fsl/FEAT
registration to register example_func and orig.mgz. Can the flag --fslregout or
--fsl do it?
Question 2: These numbers appear in the terminal whenever I click a poi
Hello, Freesurfer group,
Could you tell me the default size of smoothing extents (kernel?) of smooth1
and smooth2 in the auto-recon-all? How can I change the size with mris_smooth
in the auto-recon-all flow? And why does the smoothing not affect the thickness
measure?
Thank you in advance,
X
Hi everybody,
We have a set of patients who were all run using the same freesurfer
version, except that some of the patients had their dicom files
converted to 001.mgz with a somewhat older version of freesurfer. For
example some of them went through that step with version 4.0 or 4.0.2 or
4.0
-- Forwarded message --
Date: Tue, 13 Jan 2009 12:49:20 -0500 (EST)
From: jgre...@nmr.mgh.harvard.edu
To: a...@nmr.mgh.harvard.edu
Subject: [All] postdoc in Harvard Psych Dept.
Hi, All,
I'm looking for a postdoc to start Summer/Fall '09
This is for fMRI and/or TMS studies of m
yes, those look good to me
On Tue, 13 Jan 2009, Kelly Silva wrote:
Hi, Bruce
I´m sending some pictures of aseg.mgz. Is this well done? Is there any
objective and specific criteria to separate the cerebelum from the cortex?
Is really necessary to do the manual segmentation on that area?
Kelly,
The aseg looks good to me (as far as just those two slices go - of course
you would need to check every slice). I'm not sure I understand your
question about separating them. As far as FreeSurfer's goal, this looks
like a good result.
Allison
--
On Tue, 13 Jan 2009, Kelly Silva wrote:
no, that's right. Does the example_func have a positive determinant?
Wang, Xin wrote:
Hello, Dr. Greve,
I used brain.mgz of freesurfer after mri_converted it to nii.gz as
highres in feat registration with the thinking that the brain.mgz is
the final product of freesurfer pre-processing. Using
yes, though you might have to click on the iamge window
Wang, Xin wrote:
an additional question about tkregister2: can I move both targ and mov
together when I zoomed in to a magnified view?
Thanks,
Xin
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sen
what did you use as the highres volume in feat? If you want that reg to
work, it has to be a "freesurfer anatomical volume", meaning 256^3, 1mm3
doug
Wang, Xin wrote:
Hello, Freesurfer group,
I registered the example_func.nii.gz to brain.mgz in tkregister2 using
FS/anat2exf.register.dat, a
Ming,
You can get it here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable
notice there is one for intel and one for powerpc.
Nick
On Mon, 2009-01-12 at 22:05 -0600, Ming Hsu wrote:
> Hi, is FS v4.0.5 for Leopard still available? I upgraded from Tiger
> and would like
Hi Vina,
I wouldn't worry about it.
cheers,
Bruce
On Tue, 13 Jan 2009, Vina Goghari wrote:
Hi guys,
Many of inflated brains have a little dent on the side. I looked at the
white/grey segmentations and they look good to my eye. Since you have looked
at way more of these brains I wanted to con
Hi guys,
Many of inflated brains have a little dent on the side. I looked at the
white/grey segmentations and they look good to my eye. Since you have
looked at way more of these brains I wanted to consult - is this
something I need to be concerned about that is more subtle and I need to
fix?
Hi Anderson,
we don't anticipate having the GPUs be required ever at this point.
cheers,
Bruce
On Tue,
13 Jan 2009, Anderson Winkler wrote:
Yes, Pedro, this is the idea.
We have been using FreeSurfer in a cluster, but in that setting, every node
have their own graphics card (like I think y
Hi guys,
Many of inflated brains have a little dent on the side. I looked at the
white/grey segmentations and they look good to my eye. Since you have
looked at way more of these brains I wanted to consult - is this
something I need to be concerned about that is more subtle and I need to
fix?
Hello Rysia,
I'll add a comment by calling your attention to one statistical
"subtlety". When using a DODS ("separate slopes") model in the presence
of a continuous covariate, and then examining the significance of the
group effect, the interpretation (and results) depend critically on the
meani
Anderson,
Yes, blades don't have pci slots.
The GPU usually is an addon to speed up calculation.
I won't expect it would be mandatory for processing in recon-all.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedCom
Yes, Pedro, this is the idea.
We have been using FreeSurfer in a cluster, but in that setting, every
node have their own graphics card (like I think you have at USP). For
the new system, however, the blades don't even have PCI or AGP expansion
slots, so to display, now that we know that GPUs a
Hi Anthony,
For cortical gray matter volume, compute statistics using the
{lh,rh}.cortex.label file.
i.e.,
mris_anatomical_stats -l lh.cortex.label -f $subj/stats/lh.cortex.stats
$subj lh
That will be roughly similar to computing the volume difference between
the pial and white surfaces, except
Hi Adrian,
you can always do:
recon-all -s adrian -make all
and it will redo the steps that it needs. If the bug doesn't replicate it's
tough to fix, and could be a real bug or some other issue (bad memory chip,
full disk, etc...).
cheers,
Bruce
On Tue, 13 Jan 2009, Adrian
Williams wrote:
Hi Bruce
I ran the last command issued by recon-all:
mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs adrian rh
And would you believe it ran without error! Presumably if one comes across
segmentation errors in future, the first thing is to try and replicate them?
How do I continue wit
Hi Anderson,
I don't remember if I showed you here in Sao Paulo our Freesurfer
processing.
I think you could have a cluster or for better power consumption a Blade
Server to run several recon-all at same time (don't forget to reserve at
least 1GB Ram per core)
To visualize your data you can use a
Thanks a lot for the ideas, Bruce!
On Monday 12 January 2009 23:16:30 Bruce Fischl wrote:
> Hi Martin,
>
> for the MS study we were *very* careful to make sure that the white
> matter in the regions of detected effect was normal appearing, so I don't
> think it explains the thinning we saw.
I see
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