Hi all,
I do group analysis using QDEC to detect the difference between the normal
group and the patient group, the result shows some significant difference brain
area (normal > patient, red, uncorrected p=0.001). I extract the average
cortical thickness in this area(ROI), then export tho
Hello Freesurfers
I'm starting to work with DTI data and I have a couple of questions;
I have 2 identical DTI sequences for some subjects and I would like to work
with them, does anyone knows if it's better to concatenate them or to make an
average of them?
And I'm wondering when I make a
its hard to say without more details, but if i'm reading your email
correctly, one notable difference is that you state that you extracted
the cortical thickness data for an ROI and conducted the analysis in
SPSS using that data. that would not be the same analysis as what qdec
is doing. qdec is
you also must verify that you are using the same exact model for the
analysis.
doug
Nick Schmansky wrote:
> its hard to say without more details, but if i'm reading your email
> correctly, one notable difference is that you state that you extracted
> the cortical thickness data for an ROI and co
Thank you
On Sat, Nov 6, 2010 at 1:32 AM, Martin Reuter
wrote:
> Hi,
>
> as mentioned before, target for 5.1 is still end of November.
>
> Best, Martin
>
> On Thu, 2010-11-04 at 19:40 -0400, Bruce Fischl wrote:
> > Martin is the one to ask
> > Bruce
> > On Thu, 4 Nov 2010, Alan Francis wrote:
> >
Hi Freesurfers,
Anybody knows how can I make lh and rh.annotation.aparc files for a monkey?
I
need them initiate an brain averaging process.
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
__
Hi Shahin
you'll need a monkey atlas based on manually labeled monkey folding
patterns. we don't have one, but it's possible that someone else on the
list does (it would be a lot easier to do for monkey than it was for human
as the folds are so much simpler)
cheers
Bruce
On Mon, 8 Nov 2010,
Hi Shahin
have you run spherical registration? If so, to what target? I don't think
the monkey-to-human atlas aligment is that robust, so you would need a
monkey geometry atlas (which is a lot easier to build as you don't need to
do manual labeling for it). Probably someone on list has one?
Thanks Bruce,
To avoid this problem, is there anyway to run make_average_subject without
having lh and rh.aparc.annot files?
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
From: Bruce Fischl
To: Shahin
C
Yes, I have made a template on the basis of many monkeys
(mris_make_template) and then I have done spherical registeration for each
individual monkey (to this template) by using mris_register. Now it is the
final
step and I have to run the make_average_subject but it generates an error
say
It is needed in make_average_surface. I've created a new version that
does not use the aparc (thought I have not tested it). You can get it
from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
Make a backup of your current version of make_averag
Hello Freesurfers
I'm starting to work with DTI data and I have a couple of questions;
I have 2 identical DTI sequences for some subjects and I would like to work
with them, does anyone knows if it's better to concatenate them or to make an
average of them?
And I'm wondering when I mak
You'll probably have to do it by hand with tkregister2. Someone on the
list may have solved this problem before.
doug
Shahin wrote:
> Ok now I faced another problem saying that I dont have talairach.xfm
> for monkeys. Would you tell me how can I generate it for monkeys?
>
> Shahin Nasr
>
> P
Ok now I faced another problem saying that I dont have talairach.xfm for
monkeys. Would you tell me how can I generate it for monkeys?
Shahin Nasr
PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
From: Douglas N Greve
To:
I'm trying to run a retinotopic analysis with the following commands:
mkanalysis-sess -analysis retino-lh -TR 2 -retinotopy 40 -paradigm
rtopy.para -funcstem fmcpr.sm5.self -surface self lh -mcextreg -runlistfile
retRuns -fwhm 0
selxavg3-sess -analysis retino-lh -s somesubject -df sessdir
and am
Hi, there,
Last week, we met a problem when we ran the recon-all long-base pipeline.
%% After running this command with FS v4.5 :
recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp
005_S_0221v2_45_20061006.104318_1 -all -force
%% I get the following error:
mri_concatenate
Thanks for the hint,
Will take a look and let you know.
Martin
On Nov 8, 2010, at 10:06 PM, Guang Zeng wrote:
> Hi, there,
>
> Last week, we met a problem when we ran the recon-all long-base pipeline.
> %% After running this command with FS v4.5 :
> recon-all -base 005_S_0221BASE -tp 005_S_0
Hello,
I am a new freesurfer user and am interested in the subcortical volumetric
segmentation procedure that is used, particularly relating to the hippocampus.
I am finding it difficult to decipher exactly what freesurfer does in relation
to Talairach registration, I've read that there is an
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