Dear freesurfer experts.
is it possible for tkmedit to display volumes in neuroscience format (R is R)
rather than radiologic format (R is L)?
Thanks
Jon
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no, sorry
On 04/22/2015 12:25 PM, Jon Alan Wieser wrote:
Dear freesurfer experts.
is it possible for tkmedit to display volumes in neuroscience format
(R is R) rather than radiologic format (R is L)?
Thanks
Jon
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Hi Freesurfers,
Is there a way to generate patch files from surfaces outside of tksurfer?
I'm specifically hoping that there is some tool that will allow me to use a
label file to define the part of the surface I want to keep as a patch.
Thanks!
Michael
It is done by a nonlinear morph (encoded by ?h.sphere.reg). Not a simple
matrix.
doug
On 04/22/2015 03:01 AM, pfannmo...@uni-greifswald.de wrote:
Dear Experts,
if functional volume data are mapped to cortical surfaces, using mri_vol2surf
and FsAverage as the target surface, a surface
You need to run
recon-all -s subject -qcache
doug
On 04/21/2015 06:34 PM, Manish Dalwani wrote:
Hello Freesurfers,
In the past I have been able to run QDEC v 4.5 on images without any
problem. Recently I ran recon-all on some new set of images. I was
able to run the regression analyses
On 04/22/2015 04:27 AM, Milde, Christopher wrote:
Dear Freesurfer Experts,
is there an easy way to update only folders within the Freesurfer
folder? Accidentally, I deleted the fsaverage folder from the
Freesurfer version. I copied the fsaverage folder from another
Freesurfer
On 04/21/2015 03:26 PM, Dan Goldman wrote:
Thanks for this. I should be more clear. The reasoning and figures
tasks are completely separate and are not being compared to each
other. Each task has two conditions. For example, in the reasoning
task, I have two conditions: Spatial and
Hi FS experts,
I was wondering whether there is a tool to measure the kurtosis and
skewness of an ROI. (For instance would the mri_kurtosis.m script under
the FS home directory be the best option for the measurement of kurtosis?)
Thanks in advance,
Panos
Thank you Doug!
Manish
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, April 22, 2015 8:58 AM
Subject: Re: [Freesurfer] QDEC failed due to missing files
You need to run
recon-all -s subject -qcache
doug
On 04/21/2015 06:34 PM,
Yes. I've attached mri_skew.m as well. There are several ways to
estimate kurtosis, make sure mri_kurtosis is doing what you want.
On 04/22/2015 01:48 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS experts,
I was wondering whether there is a tool to measure the kurtosis and
skewness of an ROI.
Hello,
I am interested in using TRACULA for my data, but I have a few questions about
modifying the dmrirc configuration file. I have already conducted eddycorrect,
bet, and dtifit in FSL, registration of T1 and dti using ANTs, and I have also
registered individual subject data to a
Hi all,
I am attempting to process some 4T images that have a pretty bad signal/noise
ratio. When running autorecon 1, Freesurfer has gotten stuck on this step:
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 silvj001a rh
I am seeing that 125 defects to be corrected” and
Repost.Thanks.
On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote
Thank you again for your reply.
For editing aseg.mgz, as mentioned in
https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations
it does suggest using
Please repost this position for us.
Thank you.
*Research Assistant II (Non-Clinical) Position*
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Repost.Thanks.
On Mon, 20 Apr 2015 16:21:38 -0700 lt;pras...@zoho.comgt; wrote
Thank you for your reply.
Yes, I'm finding that it is only small edits that are required in the Long for
the case of pial surface errors. It is usually in areas where no editing was
required in the
Hi Clara,
The method for dealing with the crossing medial surfaces that works for me is decribed in the email below. Though, Im not sure if there areany issues or concerns with this approach particularly in regard to thickness or the segmentations.
Paul
Sent:Tuesday, October 22, 2013
Hi Anastasia,
I am trying to run the command trac-all with the flag -stat as mentioned in
wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics)
but I am receiving and ERROR message that this flag unrecognized. Any
suggestions please.
Mohamad
yes, it is available with the FreeSurfer source code, which you can download
doug
On 04/22/2015 04:30 PM, Patrick Beukema wrote:
Hi,
Is it possible to get the source for optseq2. I would like to
translate it into python to integrate it into my existing scripts, and
also modify the output
Hi Lee,
Thank you. But I don't have permissions to overwrite files on the cluster. I am
already using Freesurfer 5.3
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lee Tirrell
Sent: Wednesday, April 22, 2015
Hi Noreen
look at the orig.nofix or the inflated.nofix and see if there is a giant
defect caused by something like a spurious attachment between wm and the
skull or cerebellum. If so, you'll need to correct this manually either by
editing the wm.mgz or adding control points
cheers
Bruce
Hi,
Is it possible to get the source for optseq2. I would like to translate it
into python to integrate it into my existing scripts, and also modify the
output files to include csv output options, instead of writing post hoc
scripts to change the output.
Thank you,
Patrick
Dear Experts,
if functional volume data are mapped to cortical surfaces, using mri_vol2surf
and FsAverage as the target surface, a surface registration is carried out. As
far as I can see the program surfreg does the surface registration. In this
registration the cortical maps of the
Dear Freesurfer Experts,
is there an easy way to update only folders within the Freesurfer folder?
Accidentally, I deleted the fsaverage folder from the Freesurfer version. I
copied the fsaverage folder from another Freesurfer installation. But seemingly
some essential files (e.g. perirhinal
Dear colleagues,
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