Hello again!
Firstly, let me thank you for your precious previous advices, which pointed
me in the right direction.
I have another question for you: I have read your article on Reliability of
MRI cortical thickness measurements and its relation with scanner and field,
and I would like to know wha
Hi Joao,
I think we did all the subtractions and such in matlab. There are .m files
for reading/writing most of our formats.
cheers,
Bruce
On Thu, 1 Jun 2006,
Joao Pereira wrote:
Hello again!
Firstly, let me thank you for your precious previous advices, which pointed
me in the right dire
Hello !
I work for the department of Anatomy
(http://www.medecine.unige.ch/GRAC/) in the Centre Médical Universitaire
of the Université de Genève (http://www.unige.ch/).
We're planning to use the FreeSurfer software suite (or more precisely,
the surface-based stream ) in a project that aims to sy
Ivan,
In response to your first question about sequence parameters for optimal
segmentation, we achieve optimal gm/wm segmentation using the MP-RAGE
sequence protocol. For info, see Data Requirements section of this
page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
which
On Thu, 1 Jun 2006, Ivan Blagoev Topolsky wrote:
Hello !
I work for the department of Anatomy
(http://www.medecine.unige.ch/GRAC/) in the Centre Médical Universitaire
of the Université de Genève (http://www.unige.ch/).
We're planning to use the FreeSurfer software suite (or more precisely,
the
Hello all,
I get a directional cosine error when I try to register data
or extract values from them so I tried mri_info and
get this message:
mri_info subj1.img
matfile: only read
256 bytes of name (810698068 specified)
MatlabRead: readHeader returned NULL
WARNING: analyzeRead
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
1.117 0.005 0.077 -0.516;
-0.015 1.062 0.148 -22.126;
-0.084 -0.173 1.230 -34.192;
0.000 0.000 0.000 1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_3
can you run:
mri_info nu.mgz
and send us the results?
thanks,
Bruce
On Thu, 1 Jun 2006, Frederick Powell wrote:
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
1.117 0.005 0.077 -0.516;
-0.015 1.062 0.148 -22.126;
-0.084 -0.173 1
Hi all,
I posted a question, but for some reason, I didn't get any response.
Please help me on this.
Here is the question.
I ran 'process volume' and 'create surface' on csurf.
The created surface (left inflated) has brain stem attached to it.
So, I editted 'wm' slices to get rid of it, and ran '
Nam,
The csurf application is no longer supported (and has been removed from
the newest release). The recon-all script now performs all processing
stages, where the three main stages are -autorecon1, -autorecon2 and -
autorecon3 (-stage1 is a deprecated option).
You may want to see our new tutor
If you have a tkregister registration file called subj1.mat, then name
it something else as the volume reading tools think that is an
spm-style .mat file and try to read it as a matlab4 matrix.
doug
Nguyen, Thang Q wrote:
Hello all,
I get a directional
cosine erro
it is in the mri dir:
/Users/frederickpowell/freesurfer/subjects/011106RJ/mri/nu.mgz
On Thu, 1 Jun
2006, Frederick Powell wrote:
gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz:
No such file or directory
mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz
gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz:
No such file or directory
mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz,
-1): read error
I went into my subjects directory and to the subject that I ran with
the error and received the above.
--
Frederick
Dear all,
I have processed all my data using Stable v3.0.1. Does the eTIV bug
effect any other volume measures? If I want to compute eTIV for my
data, should I install the lates version and re-run mri_label_volume
-eTIV ?
Thanks,
Sasha
Disclaimer:
The materials in this e-mail are private and
Hello,
I was wondering if there is a more intutive way than
guess-and-check to help me to eliminate the distortion
on the flattened surfaces. I know that it is due the
the placement/length of the cuts, but I am not sure
how to alter the cuts so that the images won't be
distorted. This seems like
Sasha,
The eTIV bug (fixed in v3.0.2) affects mri_label_volume and
mri_segstats. mri_segstats is run as part of the standard recon-all
stream, and incorporates the eTIV calculation, putting the results in
the file subjid/stats/aseg.stats, the lines beginning with:
# Measure .
So you would n
Thanks, Nick,
If I install a new version of FS, would it be too much of hassle?
Because I am in the middle of data analysis for a project using the
old version, and I remember I had a big trouble installing different
libraries for Freesurfer for the old version, which was a daunting job.
Nam.
Nam,
The newer versions of freesurfer (those within the past year) contain
the major libraries and toolkits upon which freesurfer depends
(Tcl/Tk/Tix/BLT, GSL, MNI, FSL), so it should be straightforward to
install a new version. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
Basicaly, j
Folks:
Both tkmedit and tksurfer have tool windows which jump to a location below
their respective main image windows whenever the image windows are moved or
adjusted.
This prevents the image windows from being enlarged to full screen height,
because the tool windows then jump to bottom of s
> Both tkmedit and tksurfer have tool windows which jump to a location below
> their respective main image windows whenever the image windows are moved or
> adjusted.
>
> This prevents the image windows from being enlarged to full screen height,
> because the tool windows then jump to bottom of
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