THX for your response.
I have never move fs files. but i had a MATLAB 2011b, because of the virtual
machine`s 32 bit.
May this do harm? Or I don't configure the mat lab rightly?
here is the startup.m in ~/fsuser
% FreeSurfer -%
fshome = getenv('FREESURF
On the surface it seems like you moved the FS directory from one pathway to
another. If you place FS back into your applications folder, it may work. Also,
if you have Matlab 2014b or 2015a installed, it won’t work. You need
2012b-2014a for the process to run.
Hope this helps in any way.
Noah
Hello Freesurfers
I meet a problem in calculate Lgi
I run fs in vituralBOX, matlab is installed. At the begining everything seems
fine .but error come in "make_outer_surface". The details are in below.
=
xubuntu-VirtualBox:~> recon-all -s test001 -loc
Hi Surfers and Doug,
I was trying to average two scan sessions of the same subject and
isxconcat-sess under dev-env failed again. This time I get this message:
ERROR: cannot find
/autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2.
Hi Georg
if you have a volume (like the 001.mgz) that is in scanner coordinates
you can use the "reslice like" and "resample type" flags in mri_convert:
mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz
cheers
Bruce
On Mon, 6 Jul 2015, von
Polier, Georg wrote:
> Dear FreeSurfers,
>
Hi Anastasia,
Thanks for the clarification. I am happy to hear that you are working on that!
As the byvoxel data includes MNI coordinates, I though it could be possible to
assemble them to MNI 3D space.
Thanks again!
Pedro Rosa.
On Monday, July 6, 2015 at 12:19 PM, Anastasia Yendiki wrote:
>
Dear FreeSurfers,
I need to convert an FS-volume back in scanner space (to calculate overlap with
manual segmentation).
I went through the wiki-entry and converted to native space with mir_vol2vol,
however the coordinates are still RAS and not identical with the original
Scanner-coordinates.
Hi FreeSurfers,
I have a question regarding data visualization:
Instead of presenting population average cortical thickness overlay of
the right hemisphere on the right and of the left hemisphere on the
left,
Id like to show thickness data from epileptogenic hemisphere on one side
(lets say l
it sounds like you ran out of memory. Were other things running on the
machine at the same time? How much ram does it have?
On Mon, 6 Jul 2015, Park, Jung Mi wrote:
> Hello Freesurfer expert
>
> Recon abruptly terminated with error message
>
> from the recon-all. log:
>
> #@# Skull Stripping Mon
Hello Freesurfer expert
Recon abruptly terminated with error message
from the recon-all. log:
#@# Skull Stripping Mon Jul 6 13:16:25 EDT 2015
/autofs/cluster/scratch/monday/jungmi/anat_subjects/r0401AG/mri
mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1
-brain_atlas
Hi Yawu,
no, that would be the simple average.
Temporal average is the linear fit (within each subject) evaluated at
the mid time. So if you had 10 time points at the same day and 1 a year
later, it would look like a .5 years time point. This is used to compute
symmetrized percent change, repr
Forgot to reply re: merging. You have to merge them yourselves, sorry.
On Mon, 6 Jul 2015, Harms, Michael wrote:
Hi Anastasia,
We are looking at running TRACULA on some data, where we were attracted by the
longitudinal component of TRACULA. Is a paper on the longitudinal
aspect of TRACULA i
Hi Michael - Thanks for finding longitudinal tracula attractive! :) The
paper is under review. There's an ISMRM abstract that I can send you.
About the cluster customization: bedpostx_mgh and fsl_sub_mgh are
supersets of bedpostx and fsl_sub, so they have all the original
functionality of th
Hi Anastasia,
We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA. Is a paper on the longitudinal aspect of TRACULA in the works?
If we have multiple dMRI runs/series
per imaging session, do we need to merge/concatenate thos
Hi Pedro - The point-wise stats from tracula are a 1D sequence of values,
so they cannot be analyzed with functions that work on 2D data on the
surface or 3D data in the volume. At present, you'd have to do a seperate
analysis for every point along the tract. It's on my list to implement a
mo
Hi Freesurfer experts,
I am still trying to resolve the problem detailed below. It seems my version of
reg-feat2anat is not working properly since it does not created the
anat2exf.register.dat file needed to view fmri data analysed with FSL on the
subjects native surface in FS.
Doug posted a
glad to hear it
Bruce
On Mon, 6 Jul 2015, Clara Kühn wrote:
Hi Bruce,
it worked! The surfaces now look so much better.
Thanks for your help!
Cheers, Clara
- Ursprüngliche Mail -
Von: "ckuehn"
An: "Freesurfer support list"
Gesendet: Dienstag, 30. Juni 2015 17:18:26
Betreff: Re: [Free
Hi Clelia,
I think the reviewer might refer to the -3T flag of recon-all which enables
3T-specific NU intensity correction parameters and usage of a special atlas for
Talairach alignment.
Best,
Falk
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im
Hi Bruce,
it worked! The surfaces now look so much better.
Thanks for your help!
Cheers, Clara
- Ursprüngliche Mail -
Von: "ckuehn"
An: "Freesurfer support list"
Gesendet: Dienstag, 30. Juni 2015 17:18:26
Betreff: Re: [Freesurfer] too much white matter
Hi Bruce,
yes, it is an mp2rag
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