Dear developers/users,
This is completely ridiculous known issue on a low resolution monitor :(
Presumably, it was solved here:
http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer, but the file is
inaccessible via ftp.
Any other workaround? All I need is to change Min statistic threshold and
hit app
To add on to Bruce's explanation, the freesurfer parcellation atlas
(which for example specifies the probability of precentral gyrus at a
particular location) is not symmetric, thus it will treat the left and
right hemispheres of your subject differently if you flipped it.
--Thomas
On Sun, Jun 17
I am assuming you are on a OSX box which has that stupid protection.
Just open a Terminal and run
cat > $FREESURFER_HOME/.license
then type in the 3 lines and Enter and then do a Control-D to exit
-- Paul Raines (http://help.nmr.mgh.harvard.edu)
On Sun, 17 Jun 2012 1:45am, Monica Girald
If FreeSurfer on Mac has been installed on /Applications you may need to
type
sudo cat > $FREESURFER_HOME/.license
and enter your account password when asked
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Teleco
hello!
i am able to run mris_register on all of the OASIS brain images that i have
tested except for one: OAS1_0061_MR1:
mris_register -curv OASIS-0061_MR1/surf/rh.sphere
templates/freesurfer/rh.OASIS_template.tif
OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg
using smoothwm curvature for
Hi Arno
can you load that sphere file in tksurfer? And run mris_info or
mris_euler_number on it? I'm wondering if it is corrupted.
Bruce
On Mon, 18 Jun
2012, Arno Klein wrote:
hello!
i am able to run mris_register on all of the OASIS brain images that i have
tested except for one: OAS1_0
aha -- it seems that just the .sphere files, not the .pial or .white files,
are corrupted. is there an easy way to generate just the .sphere files
again?
cheers,
@rno
On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl
wrote:
> Hi Arno
>
> can you load that sphere file in tksurfer? And run mris_in
Hi Vadim,
When you enter the new min statistic threshold, you can hit the spacebar
to apply.
-Louis
On Mon, 18 Jun 2012, Vadim Axel wrote:
> Dear developers/users,
>
> This is completely ridiculous known issue on a low resolution monitor :(
> Presumably, it was solved here:
> http://surfer.nmr
sure. The mris_sphere command line should be in the recon-all.log file
in the subject's scripts dir. Either run that directly, or look at the
recon-all help to figure out how to do it through recon-all
cheers
Bruce
On Mon, 18 Jun
2012, Arno Klein wrote:
aha -- it seems that just the .spher
Freesurfers-
When choosing the simulation type does the ending have to match the sim
sign? for instance i see examples with
--sim mc-z 1 3 mc-z.pos.3 --sim sign pos
or
--sim mc-z 1 3 mc-z.neg.3 --sim sign neg
I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3
me
hi fellas,
i am trying to run mri_cnr command in freesurfer to compute and see CNR for
gray/white/csf the command gives following info as help:
-bash-3.2$ mri_cnr
usage: mri_cnr [options]...
-s
i understand that 'surf directory'= subjects 'surf' folder ; but i am not able
Hi KK
this is something i wrote for myself, but you are welcome to try it out.
YOu don't need to give it the slope stuff, that is optional. The "vol"
command line parms are the volumes that you want to assess CNR in. For
example:
mri_cnr ~/local_subjects/bruce/surf ~/local_subjects/bruce/mri/n
thanks Dr. B.that helped a lot
- Original Message -
From: "Bruce Fischl"
To: "Kushal Kapse"
Cc: "freesurfer"
Sent: Monday, June 18, 2012 2:27:29 PM
Subject: Re: [Freesurfer] mri_cnr
Hi KK
this is something i wrote for myself, but you are welcome to try it out.
YOu don't need to g
Did anyone else happen to see this ridiculous story on Gizmodo today?
http://gizmodo.com/5919149/your-brain-scan-looks-different-on-mac-and-pc
It cites the recent article "The Effects of FreeSurfer Version,
Workstation Type, and Macintosh Operating System Version on Anatomical
Volume and Cortical
Hello,
We are working with previously acquired data, so unfortunately we are unable to
use the MPRAGE sequence for the current data set.
We would like to use T1 images to compute volumetric results. We are using a
Philips 3T Achieva, and the sequences received by most participants are a
T1-FF
That is just the name. It must be different for each call so that the
files are not overwritten. It does not have to match the sign, but it
will be less confusing if it does.
doug
On 06/18/2012 12:38 PM, mdkrue...@uwalumni.com wrote:
> Freesurfers-
>
> When choosing the simulation type does the
Hi, FreeSurfer experts
I used mri_make_surface_parcellation and parcellated the brain into 200 ROIs.
Then some measures were derived based on the ROIs and now I have 200*1 matrix
with each ROI having a value. What I want to do is to map the ROI-based
measures back to the surface files and show t
Hello Freesurfers,
I have created an ROI label for 80
subjects in qdec. My question is the following: Is there a command
that will create a .stats file for all my subjects rather than using
the below command on each person individually?
mris_anatomical_stats -l rh.ento.label \ -t rh.thickness -b
Hi Cat, you can use something like:
mri_segstats --i y.mgh --slabel fsaverage lh your.label --id 1 --avgwf
avgwf.dat
where y.mgh is the file created by qdec that has stack of subjects' data
avgwf.dat will have a value for each subject that is the mean over your ROI
doug
On 06/18/2012 06:56 PM,
There's not an easy way to do this. You can load the parcellation into
matlab and create a matrix of size nverticesx1, then map the value you
want into each vertex, then
mri.vol = yourmatrix;
MRIwrite(mri,'lh.matrix.mgh')
then load that lh.matrix.mgh as an overlay in tksurfer
doug
On 06/18/2012
Hi!
We have an algorithm developer position open. Below is the job description.
Although it stats in a very general term, the person will spend most of time
working on freesurfer related algorithms and services.
Experience in PhD or Post doc did count as long as it is related to algorithm
deve
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