Dear all,
I run the surfcluster analysis (mri_surfcluster). But the tutorial tells me
that there exists also mri_volcluster:
Using the outputs from the estimation step and the simulations,
mri_surfcluster (or *mri_volcluster*) will create two outputs: the summary
file with a table of the cluste
Hello,
I'm having troubles trying to obtain only
the brain in T1-weighted RM images that contain metastases.
First of all I have converted the DICOM images to mgz
with "mri_convert /usr/local/freesurfer/subjects/A0D0C0.dcm
/usr/local/freesurfer/subjects/case1.mgz" . Then, I have employed
Hi,
Thank you for a good freesurfer course in Copenhagen. After the course i
have been wondering if there is available litterature regarding manuel
editing versus non-manuel editing?
Has any studies investigated the outcome/results from manual editing versus
non-manuel editing on the same sample
Dear Kasper,
I am glad you enjoyed the course.
Mikael Agn, a former master student at NRU, did a small study in his
master thesis
(http://www2.imm.dtu.dk/pubdb/views/publication_details.php?id=6647) in
section 5.3 where he investigated manual edits vs. no manual edits on
the same sample.
I h
Dear Doug,
Finally, I was able to solve the 3dvolreg.afni error problem. I installed the
recent AFNI version for Linux and replaced the 3dvolreg file in Freesurfer/bin
by the AFNI 3dvolreg.afni of the AFNI software package. After adding the Suffix
.afni (the AFNI-3dvolreg file doesn't end with
Hello,
I still cannot solve this issue. All help will be appreciated.
I am running Qdec analysis on about 100 subjects and correcting with FDR. Once
I do this I click the "find clusters and go to max" button and Qdec gives me a
plot of all the data as well as taking me to the max vertex in the
Dear Christian,
Thanks a bunch for this answer. I ran all the steps you mentioned
(except for the one where I simply do uncorrected/corrected, as these
images have different dimensions, it seems nu3 does more than just
normalization of intensities, but also image cropping). Do you know
anythin
The documentation for the 5.2.0 release (2Mar2013) states that -openmp works
for the CentOS 6 distribution only.
Is this still the case?
Or does it work for CentOS 7 ? any other Linux version ?
Thanks,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648
Hi Gamaliel
do you mean a skull model? If so, you might check out Matti Hamalainen's
MNE package, which is built on top of FreeSurfer surfaces.
cheers
Bruce
On Wed, 27 Aug 2014, gamaliel huerta urrea
wrote:
Hi
I have questions about the use of the function:
mri_make_bem_surfaces
I
Hi Barbara,
you should just be ble to divide the original image by the nu-corrected
one to get the estimated bias field.
cheers
Bruce
On Wed, 27 Aug 2014, Barbara Kreilkamp
wrote:
> Dear all,
>
> Is there a way to output the N3's (non-parametric normalization step)
> output?
> I am interested
Hi Barbara
what exactly did you divide? If you look at the recon-all.log it will
show the exact inputs and outputs of nu_correct.
cheers
Bruce
On Thu, 28 Aug 2014, Barbara Kreilkamp wrote:
> Dear Christian,
>
> Thanks a bunch for this answer. I ran all the steps you mentioned
> (except for the
Dear all,
I've run selxavg3-sess and I got this error message when it tried to
read the fmcsm file (fmc.sm5.DM.lh.nii.gz).
Thank you for your help,
Francesca
shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy>
selxavg3-sess -a rtopy.DM.lh -s SUBJ01
Surface data DM lh
--
Dear Bruce and Christian,
I found the easy way of simply writing 'set cleanup = 0' at the
beginning of mri_nu_correct.mni and then I run this command
mri_nu_correct.mni --i T2-scic/mri/orig/001.mgz --o nu.mgz --n 2
This way I get all the masks and iterations that were computed.
Now I also see t
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Hi Don,
Support of openmp is determined by the compiler used to build the code.
gcc4.2 and greater support openmp.
So the centos6 build does support the openmp flag but the centos4 and
centos4_x86_64 version of freesurfer do NOT. We do not yet build on
centos7 but once we do it surely will sup
Thanks, Zeke.
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Z
Thanks. I see that the older ones were done on freesurfer 3.0.2. I am assuming
there are not many differences between the segmentation process between 3.0.2
and 3.0.3 so I downloaded 3.0.3 because 3.0.2 is no longer available. I set
freesurfer_3.0.3 as the default version and started a recon-all
Hi,
I couldn't find the documentation for mri_preproc. I know that roughly it
resamples multiple subjects' brain images into the same space and then
concatenates the vertices, but I want to know details like:
Exactly how are the brains resampled? What is the procedure beyond the
Talairach affine
Hi Matt
you might want to email Matti about this. I think that you can, but he
might know the details
cheers
Bruce
On Tue, 26 Aug 2014, Sherwood, Matt wrote:
Freesurfer,
We have scans that have recon-all completed. Following
recon-all, we completed watershed (under the MNE
Hi Vincent
I would say yes. If the skull stripping leaves dura in one image and not
in the other, then that could cause big differences as the surface
deformation grabs it when it is present.
cheers
Bruce
On Tue, 26 Aug 2014, Vincent
Beliveau wrote:
I've attached ?h.orig.nofix for both r
I am trying to create a spherical ROI mask in the form of a volume file with
2.5 cm radius. I also have to specify the center of the ROI location. What is
the best way to accomplish this?
I intend to use this to extract freesurfer cortical thickness values for a
region-of-interest (ROI) defined
Hi Juan
probably the easiest thing to do is to create an empty volume (in e.g.
freeview) with the same geometry as one of our conformed ones, Then run
through every voxel in matlab and if its Euclidean distance to your
specified center is less than 2.5cm set it to 1, otherwise set it to 0.
c
Hello Experts,
I was wondering if there is a way to short time of recon-all; I see that by
using some of the parameters, one can get rid of different outputs. For mne
forward models and inverses is there a recommended list of necessary and
unnecessary outputs?
Isaiah Smith
Dear Michele,
I cannot find anything wrong with your bvec and bval files.
Seeing as you had an errormessage related to the dwi (the one about the
dwi_frame.nii.gz): Did you check that your dwi data have the same amount
of volumes as entries in bvec and bval?
Good luck,
Barbara
On 28/08/2014
Hi Isaiah
sorry but no, there is no easy way to shorten the processing time except
to use multiple processors and open MP
cheers
Bruce
On Thu, 28 Aug 2014, Isaiah C. Smith
wrote:
> Hello Experts,
>
> I was wondering if there is a way to short time of recon-all; I see that by
> using some of
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