Hello Freesurfers
I still have the problem using a tcl script that should load the pial
surface on a patch in tksurfer. I tried to use the following three
commands:
1. set gaLinkedVars(vertexset) 3
SendLinkedVarGroup view
redraw
2. read_pial_vertex_coordinates
redraw
3. read
what may have gone wrong.
>> See attached screenshot from tkmedit.
>> Any suggestions how to fix this would be helpful.
>>
>> I have processed other datasets collected from the same scanner using the
>> same sequence which seem to have correctly identified the pial and
>>
Hi Iris,
updating. I would try:
set_current_vertex_set 3
UpdateLinkedVarGroup view
UpdateAndRedraw
if this doesn't work, tell us, and if you don't get a response in the next
day or so, can you repost in a week? We are flat out trying to prepare for
our upcoming course and also get 5.1 out th
Hello,
I am running into an issue with running preproc-sess on OSX as outlined here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15896.html
I saw Doug posted a bug fix that should solve this problem, however, I am
unable to access it from:
ftp://surfer.nmr.mgh.harvard.edu/transf
YORK UNIVERSITY
Job Type: Contract
Location: Toronto, ON, CANADA;
Industry: Education
Company URL: http://www.yorku.ca
Date Posted: March 31, 2011
JOB TITLE: MRI Analyst, Neuroimaging Laboratory
TYPE OF POSITION: Contract – 1 year contract with a possibility of renewal
SALARY: $60,000 - $75,00
Hello FS Experts,
Suppose we have two points on the cortical surface (pial for example), we want
to know the distance between these two point along cortical surface (not direct
distance). Does FS report this kind of distance? Any suggestion will be very
appreciated.
Aize
Hi Lan,
this tool will be available in 5.1
Martin
On Wed, 2011-03-30 at 11:03 -0700, lan lin wrote:
> I installed freesurfer 5.0 and want to use long_mris_slopes to prepare
> the longitudinal data but couldn't find the command. Where can I find
> it?
>
> thanks
> Lan
>
This question comes up sometimes -- and the short answer is 'yes', there
is a tool that can allow you to do this. Although it will be available
in the next version of FS (5.1), it is still a bit rough around the
edges. It is called 'mris_pmake' and to use it to determine the distance
between two po
Thanks, Doug and Michael--that did the trick! What is the status of this
issue for newer versions of FreeSurfer (e.g., 5.0)?
Tyler
On Tue, Mar 29, 2011 at 8:17 AM, Douglas Greve wrote:
>
> As Michael says, with spm8 you have to use nifti. When 4.5 was written,
> spm8 was not around (or not used
It is very good to know FS has this function. It will be very helpful for us.
Thanks.
Aize
> Date: Fri, 1 Apr 2011 13:57:23 -0400
> From: rudo...@nmr.mgh.harvard.edu
> To: caoa...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Distance between two points along c
Hi guys,
i am using the freesurfer-fsl integration to use labels from the freesurfer
cortical surface as seeds for probtrackx
probabilistic diffusion tractography. when the output of probtrackx is
generated it is already in the freesurfer
conformed space. I want to resample the output of probtr
Hi Aize,
great circles on the ?h.sphere should be within about 15% of the true
geodesic distance. We routinely use them to estimate distances.
cheers
Bruce
On Sat, 2 Apr 2011, caoaize wrote:
>
>
> Hello FS Experts,
>
> Suppose we have two points on the cortical surface (pial for example), we
>
Hi Knut
does the file brain.mgz exist in $SUBJECTS_DIR/004/mri? If so, can you run
ls -l $SUBJECTS_DIR/004/mri/brain.mgz
Bruce
On Thu, 31 Mar 2011,
Knut J Bjuland wrote:
> i used the following command to repeat a failure output. i used just one
> subject to get a fast output since my pc is
Hello Freesurfers,
I am happy to find out that it is possible to carry out vertex-by-vertex
analyses for specific ROIs. Can someone help me understand,
1. How to run such a vertex-by-vertex analyses for certain ROI or ROIs?
2. Can we apply cluster-wise correction or FDR to the ROI to correc
Hi there,
I'm having difficulty creating labels in tksurfer (v4.5). I followed the
"Creating Labels" instructions on the Wiki, however clicking Fill on the
closed path didn't seem to do anything. I used save label anyway, and tried
to load this new label again, and even though it says "7681 nonze
Hi Ilana,
usually a bizarre labeling means the annot is out of date. Try running
recon-all with -make all on that subject and see if it needs to recreate
anything.
Not sure what's up with your label, but things can act strangely when the
surfaces are out of date
cheers
Bruce
On Fri, 1 Apr 201
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