dear freesurfer experts,
I tried to install freesurfer in a remote linux cluster, when I completed the
installation, and began to run the freesurfer gui use my own windows PC, the
command line showed erro belowing information :
[wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz
GLUT: Fatal E
Hi bruce,
I want cortical thickness, total surface area, instrinsec curvature index and
folfing index.
VP
Date: Wed, 20 Mar 2013 13:09:54 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
it dep
Hello all,
I am starting to run some analysis using fs-fast and I had a few basic
questions that I couldn't find answers on the wiki/tutorial.
1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat
What is the format of the input file for -tpexclude? Is it simply a single
column of intege
There are chunks of the brain missing from the brain mask. This may cause
some tracts to be incomplete or missing.
But you should still check that the gradient directions are correct, so
you know if you have multiple problems or just one. The FA map can't tell
you if the gradient table was c
They are the input (mri_glmfit --y y.mgh) averaged over the clusters.
They are raw input, no detrending.
doug
On 03/20/2013 05:16 PM, Laura M. Tully wrote:
> Hello experts,
>
> could someone clarify for me what the y values in the xxx.ocn.y.dat
> files represent following glmfit-sim? are they the
Thank you Anastasia. I'm checking gradient table but I would like underline
that I'm noting some holes in dti_FA.nii.gz and not in dwi.nii.gz (I have
attacked the relative images).
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 16.40
A:
Cc:
Ogg: Re:
HI
I have similar problem and filled a bug report at.
Product: Fedorahttps://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy
Franklin changed: What |Removed |Added
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Hello experts,
could someone clarify for me what the y values in the xxx.ocn.y.dat files
represent following glmfit-sim? are they the residualized y values of avg
cortical thickness in that specific cluster after regressing out the effect
of any predictor variables in the glm?
Thanks!
Laura.
--
Hi all,
My RA's are having similar issues running Freeview on Ubuntu (I've read
others are having the same issue). They get the following error when trying
to call freeview:
"freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
Hi John
if you email it to me I'll take a look
Bruce
On Wed, 20 Mar 2013, Ostuni, John
(NIH/NINDS) [E] wrote:
> We have a data set that mri_info cannot work with.
>
> We've tried multiple architectures and freesurfer versions, but mri_info
> either crashes with segmentation fault or generates e
We have a data set that mri_info cannot work with.
We've tried multiple architectures and freesurfer versions, but mri_info either
crashes with segmentation fault or generates errors such as
*** glibc detected *** mri_info: free(): invalid pointer: 0x006b ***
One feature of the data
Try using this version of mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
doug
On 03/20/2013 01:10 PM, Laura M. Tully wrote:
> the mri_segstats command did not work - below is the command and
> output. It looks like it is searching for the .annot file in fs
On a Mac? You can just ignore those warning messages. Unfortunately we
were unable to remove them.
Ruopeng
On 03/20/2013 04:07 PM, Glen Lee wrote:
Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf
template in either fsaverage or fsaverage_sym direct
Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf
template in either fsaverage or fsaverage_sym directory.
FYI, I'm using freeview v1.0
if anybody know, please help.
-Glen
$ freeview -f lh.inflated
2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid
Hi Sophie, you can run the following command:
cd $SUBJECTS_DIR/yoursubject
mris_apply_reg --src xhemi/surf/lh.thickness --streg
xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg
--tval surf/lh.rh.thickness.mgh
lh.rh.thickness.mgh will now have the rh thicknesses on the r
Hi FreeSurfer experts,
I would need to use the registration tools in freesurfer because the fsl ones ga
ve me some problem.
Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav
e three questions:
1) mri_ca_registration generates a talairach tansform file in .m3z format
the mri_segstats command did not work - below is the command and output. It
looks like it is searching for the .annot file in fsaverage directory. How
do I tell it to use fsaverage and to look for the .annot elsewhere?
cd glmdir
mri_segstats --i beta.mgh --annot fsaverage lh
./SZcontrast_oneGrp_o
it depends on what measures you want
Bruce
On Wed, 20 Mar 2013, Valtina Pouegue
wrote:
Hi Bruces,
It's because i'm doing a comparison between brainsuite and freesrufer. So , I
would like to export results of
segmentation with Brainsuite and make measurements with FreeSurfer. In Fact,
with f
On 03/20/2013 12:09 PM, Laura M. Tully wrote:
> Sorry - meant to respond to list.
>
> Thanks for the response Doug - I have a few follow up questions I hope
> you can clarify:
>
> * is the xxx.ocn.annot file created by mri_glmfit-sim considered
> a "label" by freesurfer?
>
It is an
Sorry - meant to respond to list.
Thanks for the response Doug - I have a few follow up questions I hope you
can clarify:
>
>- is the xxx.ocn.annot file created by mri_glmfit-sim considered a
>"label" by freesurfer? or does it need to be converted to a label before I
>can use mri_seg
In running a mass-univariate LME models analysis I keep running into calls to
the parallel computing toolbox (parfor, matlabpool, etc…). I was able to
comment out these lines in some of the scripts but I've run up to one that is
particularly difficult to modify (I am not an expert in MATLAB).
Hi Stefano - Have you checked that your gradient table is correct by
looking at the output of the tensor fit?
a.y
On Wed, 20 Mar 2013, std...@virgilio.it wrote:
Hi list and Anastasia,
if you remember the last week I had same problems with tracula output: the
final tract are lacking or
inc
Hi Benjamin - Have you checked that your gradient table is correct by
looking at the output of the tensor fit?
a.y
On Wed, 20 Mar 2013, Roschinski, Benjamin wrote:
> Dear Freesurfer users and experts,
>
> we have some problems using TRACULA. This means that tracks are missing or
> that they a
On 03/20/2013 10:17 AM, Laura M. Tully wrote:
> Hi,
>
> I wanted to re-post my questions from a couple of days ago below, but
> with some more specific questions following a search through the
> archives.
>
> I want to be able to extract the beta values from a cluster identified
> using mc-z in
Hi list and Anastasia,
if you remember the last week I had same problems with tracula output: the
final tract are lacking or incomplete for same subjects. Some of these are less
wrong (only forceps major), other have more evident error (you can see this in
picture that I have attacked).
To res
Hi,
I wanted to re-post my questions from a couple of days ago below, but with
some more specific questions following a search through the archives.
I want to be able to extract the beta values from a cluster identified
using mc-z in a group by behavioral variable interaction so that I can 1)
plo
Dear Freesurfer users and experts,
we have some problems using TRACULA. This means that tracks are missing or that
they are too short.
I hope you can advise me how to fix these problems.
Thanks and kind regards
Benjamin
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Fre
Hi Bruces, It's because i'm doing a comparison between brainsuite and
freesrufer. So , I would like to export results of segmentation with Brainsuite
and make measurements with FreeSurfer. In Fact, with freesurfer I can have more
parameters than with freesurfer. Does it exist another way for get
yes, I have it
On Tue, 19 Mar 2013, Longchuan Li wrote:
Hi, Bruce
The command line I used is:
mris_fill -r 1 -c rh.white rh.white.nii.gz
I attached the rh.white in my previous mail. Could you see it in the attachment?
Thank you!
Longchuan
__
Hi Valtina
you can try opening it with freeview if all you want is visualization. If
you are trying to produce anatomical stats you will need a lot more than
just the pial surface, as mris_anatomical_stats computes many things from
an array of inputs (such as the wm.mgz, the aseg.mgz, etc)
Hi Fs Team,
I am getting this errow while trying to use freeview.
reesurfer@freesurfer-VirtualBox:~$ freeview
freeview.bin: error while loading shared libraries: libjpeg.so.62: wrong
ELF class: ELFCLASS32
Any Help
Tx
chikku
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HI
I have copied the info from Bugzilla.
Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy
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