Thanks very much, that is what i want exactly, actually, I also tried to
created a customized LUT and just assign the ROIs specific color and make other
region to be white, It works, but It can not give me the color bar to define
the magnitude of my p values, I will try your way, actually, this
Ok, I checked out with the people who work with the transformation of the
data(transfer the original bvec and bval to the BIDS structure, i think she
made some mistake when transferring it), Thanks very much:)
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la
Dear experts,
while testing V6beta version I encountered problem with aseg. In one subject
(with quite large ventricles) posterior part of right lateral ventricle is not
labeled as brain at all and part is labeled as WM-hypointensities and
nonWM-hypointensities. Moreover, in aparc.a2009s+aseg t
Dear Bruce, Doug and the rest of the team,
I hope you have had a pleasant start of the new year!
We have noticed that there is now a 6.0.0 RC but that the modification date
changes while the file name persists. We are planning on running some
processing, but it seems to be better to hold off un
Hi Antonin,
yes, we came across that bug and have fixed it (it's one of the reasons
that we didn't release before Christmas)
Thanks for catching it thouggh
Bruce
On Wed, 4 Jan 2017, Antonin Skoch wrote:
> Dear experts,
>
> while testing V6beta version I encountered problem with aseg. In one s
Dear Eugenio,thank you very much.How can I obtain the beta version
6.0?Moreover, given that we are planning to analyze a big sample, I wonder when
will be approximately released the stable's 6.0?Thanks
Kind regards
Stefano
Messaggio originale
Da: "Iglesias Gonzalez, Eugenio"
Data: 3
I would wait for the stable release, then. The idea was to release it before
Christmas but some bugs were found.
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
On 4 Jan 2017, at 15:06,
Hi all,
I'm trying to create a label by making a circle with a fixed radius around a
defined vertex. I'm trying to use the method described here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg44098.html
I made the initial surface overlay with my vertex of interest having a valu
There is no one command that will do it. You can do it in matlab,
something like
a = MRIread('spike.mgh');
a.vol = a.vol/a.vol(yourindex);
MRIwrite(a,'spike.rescale.mgh');
Or you can get the vertices and values with
mri_convert spike.mgh --ascii+crsf
to get all the vertices and their val
Hi Tobias, we have a release candidate that we are testing now. If all
goes well, then our release date will be Jan 17 (of 2017:).
doug
On 01/04/2017 05:56 AM, Tobias Granberg wrote:
> Dear Bruce, Doug and the rest of the team,
>
> I hope you have had a pleasant start of the new year!
>
> We ha
Hello,
Is there some way to use multithread in recon-all to speed up?
I searched the freesurfer website and try using
recon-all -autorecon-all -itkthreads 8 -subjid SUBID
It simply gives an error message
"
ERROR: Flag -itkthreads unrecognized.
"
Thanks!
Best
Tengfei
The information containe
use -openmp 8
instead
cheers
Bruce
On Wed, 4 Jan 2017, Li,Tengfei wrote:
Hello,
Is there some way to use multithread in recon-all to speed up?
I searched the freesurfer website and try using
recon-all -autorecon-all -itkthreads 8 -subjid SUBID
It simply gives an error mess
great! That works.
Best
Tengfei
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, January 04, 2017 11:28 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer multithr
Dear FreeSurfer team,
Repost: Please let me know if the answers are too obvious or the questions are
inappropriate for this forum!
I'm currently doing a structural FS analysis with 50 Multiple Sclerosis (MS)
patients and 25 Healthy Controls (HC). FLAIR-lesions were drawn onto the
aseg.mgz a
I'm trying to convert a group of .dcm files to .nii.gz, but I've been getting
the following output with an error at the end...
mri_convert IM-0020-0001.dcm example.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from IM-0020-0001.dcm...
Starting DICOMRead2()
dcmf
Hello Freesurfer Experts,
My apologies if this is a rather simple/obvious question. I am trying to run 3
Monte Carlos using mri_glmfit-sim with the following commands:
Left hemisphere surface:
mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../LH_7vFix/ --sim mc-z 1 1.3
mcz1_1.3 --sim-sign abs -
Dear experts,
with V6 beta version of freeview I encountered, that when some input file
specified in command line is missing, the loading of remaining files is
stopped. This was not the case with 5.3 version. I found this feature handy. Do
you think that it would be good to implement this behav
Dear experts,
I have several questions regarding "reposition surface" tool in freeview
(V6beta):
1.
Are here any documentation how to use "reposition surface" tool? I would
especially velcome the explanation of significance of "sigma", "size" and
"gradient direction" parameter. I tried to play
Hi Robert
disk space and permissions are really the only two things I can think of.
Can you try writing it somewhere else? Or using .mgz as output (or .nii
without the .gz)?
cheers
Bruce
On Wed, 4 Jan 2017, Wujek, Robert
wrote:
> I'm trying to convert a group of .dcm files to .nii.gz, but I'
I will add a "-continue" option for this. It may not make it to the
final V6 release. But you can always download our nightly dev build of
freeview anytime.
Best,
Ruopeng
On 01/04/2017 03:38 PM, Antonin Skoch wrote:
Dear experts,
with V6 beta version of freeview I encountered, that when some
Great! Thanks for the quick response.
Best wishes,
Tobias
_
Tobias Granberg, MD, PhD
Karolinska Institutet | Department of Clinical Science, Intervention and
Technology
Karolinska University Hospital | Department of Radiology
141 86 Stockholm, Sweden
Cell
Hi Freesurfer Experts,
I have installed Freesurfer5.3 and it seems to be working fine. However when i
tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit)
results on freeview, i got the following message:
"OpenGL warning: No pincher, please call crStateSetCurrentPointers
Please could someone consider my email question sent dec 14th?
Email below
Thanks
Lucette A. Cysique, Ph.D.
NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017
NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA
Senior Lecturer SoMs, UNSW Medicine
Affiliated senior rese
Hi Lucette
how do you do the editing? Looks like it was in some other package, which
probably accounts for the error. You should be able to fix it by
cding into the mri dir and running:
mri_convert -rt nearest -rl orig.mgz aseg.your_edits.mgz aseg.mgz
cheers
Bruce
On
Thu, 5 Jan 2017, Luce
I’m not sure about the first part of the message, but "Did not find any volume
geometry information in the surface” can be ignored. It is just a warning. Did
the program still run? If so, you can ignore these warnings.
Best,
Ruopeng
> On Jan 4, 2017, at 6:49 PM, Jennifer Szeto wrote:
>
> Hi F
Thank you Ruopeng,
I manage to have Freeview loaded up but not the results from the GLM_FIT
analyses...
Jen
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Ruopeng Wang
Sent: 05 January 2017 01:19
To: Freesurfer support list
Subject: Re: [Freesu
Dear All,
I am looking to hire a postdoc to develop machine learning algorithms
for large-scale publicly available MRI and behavioral data. Experience
with probabilistic machine learning (aka graphical models) or deep
learning is a plus.
The ultimate goal is automatic scientific discovery (see re
Dear All,
I am looking for a neuroscience/psychology postdoc to apply machine
learning algorithms (possibly developed in our lab) to discover and
understand mental disorder subtypes from existing large-scale public
databases.
See recent example from our lab
(http://www.pnas.org/content/113/42/E65
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