Dear FreeSurfer experts,
in the publication 'Accurate and robust brain image alignment using
boundary-based registration', by Greve and Fischl (2009), in formula 2 a
quantity termed N occurs.
It is described as:'N is the total number of vertices participating'.
Can I find this N in the files
Dear FreeSurfer experts,
how can I increase the font size on the tkmedit scale bar?
Cheers
Joerg
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The information in
Just for completeness, I refer to my first contribution:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
On Mon, 13 May 2013 13:58:30 +0200
Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:
Hello Nick,
just installed and tested the BETA version.
In this case, you are just specifiying -per-session and not specifying
-mni305 or -surface
When you run mkanalysis-sess, specify -native instead of -mni305 or
-surface, like:
mkanalysis-sess -native -fwhm 5 ...
doug
On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote:
Hi Doug
format of the fmc files. Actually those files are
called fmcpr, if I use -per-run. How can do I have to proceed if there is more
than one run?
On Mon, 6 May 2013 10:54:54 +0200
Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote:
Thanks for your help. It works fine if one uses
preproc
Hello,
I have two different results from a paired difference analysis lets call it A
and B. How can I do a two sample t-test with those results (A-B)? Somehow I am
stuck in using isxconcat-sess on the group results A and B. Help is highly
appreciated.
Cheers Joerg
=
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
else
set subcortmask =
$FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz
endif
doug
On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote:
Hi,
if I apply the following command
Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm
-fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii
On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote:
It is attached to this mail.
On Tue, 16 Oct 2012 16:16:54 -0400
Douglas N Grevegr...@nmr.mgh.harvard.edu wrote:
can you send a pic?
On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote:
Hi Doug,
the analysis is done on the cortex
I just noticed that the data I am currently working with are from a data set in
which the freesurfer protocol for the anatomical sequence has not been used.
Instead an in-house protocol is applied.
On Wed, 17 Oct 2012 18:31:05 +0200
Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote
Hi Doug,
the analysis is done on the cortex surface. The following commands are used for
the analysis of the functional activation in the right hemisphere cortex:
preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305
-fwhm 0 -per-run -nosmooth
plot-twf-sess -s sessionID
Dear Freesurfers,
I computed the functional activation in a sensory task using freesurfer's
fsfast stream. In the cortex surface line like activated regions are present.
Their extension is much larger than the extension of the expected regions.
Therefore, I suppose that those regions are due
Dear freesurfers,
if I display fsaverage in tksurfer (tksurfer fsaverage rh pial) and switch on
the scale bar it appears to have a length of approximately 1 cm. However, If I
start to zoom into the brain the color bar shrinks until a
certain scale-up is reached. After it has completely
/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister
manually, giving a good registration result. Can you give
P.S.:I executed the following sequence to achieve the first level analysis with
a correct registration.
preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage
lhrh -mni305 -fwhm 0 -per-run
register-sess -s session_id -fsd bold -per-run -init-header
preproc-sess -s
. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister
manually, giving a good registration result. Can you give me a hint how to
modify
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually,
giving a good registration result. Can you give me a hint how to
modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
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Dear freesurfers,
I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In
the preprocessing the functional images are registered to the anatomical ones
using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the
preproc-sess registration fails it is
Dear freesurfers,
currently the freesurfer single tfl protocol for the segmentation of the cortex
surface was implemented at our scanner.
Siemens Verio 3T MRT
NumarisVersyngo MR B17
Gradientensystem (Tim 102x8) VQ-Engine
Unfortunately the echo-time (te) could not be set to the
Hello @all,
I want to segment anatomical data recorded from an experiemental sequence. This
sequence creates pictures with contrasts in a rather narrow range around two
hundred if projected into an 8bit grayscale. Freesurfer fails to segment those
data. However, if I rescale the brightness in
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