[Freesurfer] mritotal and COR files

[F.Musso]

Hello "freesurfers",
I have a very basic question...
Following the tutorial about freesurfer on the FSL home page and also the
freesurfer tutorial I try to create the talairach.xfm trasformation file
using mritotal.
But apparently mritotal don't like the COR format files.

I did several trials but always the same result:

'cannot open COR-001'

and from mincinfo I got:

'is not a netcdf file'

...

Someone can help me?

Thank you in advance

Francesco Musso

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[Freesurfer] Fw: Freesurfer new release

[F.Musso]

Hi to all,

 On the Freesurfer homepage I notice that via 'ftp' it's avaliable a new
 version of Freesurfer x Linux (26.08.2004).
 But there's nothing about it neither on the mail list nor on the
homepage...

 It's just a 'beta' version?

 Cheers

 Francesco Musso MD
Laboratory of Molecular Neuroimaging & Electrophysiology,
Department of Psychiatry,
Johannes Gutenberg-University,
Mainz, Germany


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[Freesurfer] bad segmentation [newbie]

[F.Musso]

Hi to all,

In our last analysis, among 12 subjects after "-stage 1" and "-stage 2" we
got only 3 reasonable brain surfaces.
Most of the other brains have a very odd shape:
-pieces of skull
-coharse lack of cortex
-holes
-bridges
-bad cutting planes
-cerebellar attachments
It seems to be a segmentation problem.
How to solve some of these problems is clearly explained in the
'FreesurferGuide' but the whole analysis seems to be "too much affected"!

I have to fix those errors manually?
Can repeat the -stage 1 changing some parameters in the intensity
normalization and/or segmentation process?
I attach some examples (small jpg files)

Thank you in advance.

Cheers
Francesco Musso

Laboratory of Molecular Neuroimaging & Electrophysiology,
Department of Psychiatry,
Johannes Gutenberg-University,
Mainz, Germany<><>___
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[Freesurfer] Re: bad segmentation [newbie]

[F.Musso]

Hi Bruce and Nguyen,

Thanks for your reply.
The scanner is a Sonata Siemens of 1.5 T with a new head coil -I'm waiting
the feedback from the engineer of the neurorad for more technical details
over this coil-
The following is the output of 'mri_convert' over the native scanner data
(mr.1.3.12.2.1107)
I cancel the subject name for a privacy issue :-)
---
Identification
NumarisVersyngo MR 2002B 4VA21A
ScannerModel  Sonata
PatientName   X
Date and time
StudyDate 20040630
StudyTime 182400.00
SeriesTime184547.703000
AcqTime   183813.397498
Acquisition parameters
PulseSeq  *tfl3d1_ns
Protocol  MPRAGE_sag_1.0mm_sense2
PhEncDir  ROW
EchoNo0
FlipAngle 0.261799
EchoTime  3.93
InversionTime 1100
RepetitionTime2160
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 1
SeriesNo  2
ImageNo   1
NImageRows512
NImageCols512
NFrames   1
SliceArraylSize   1
IsMosaic  0
ImgPos 90.3748 165.9758 123.3529
VolRes  0.5000   0.5000   1.
VolDim512 512 176
Vc -0.  -1.   0.
Vr -0.  -0.  -1.
Vs -1.  -0.   0.
VolCenter   2.3748  37.9758  -4.6471
TR=2160.00, TE=3.93, TI=1100.00, flip angle=15.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
Original Data has (0.5, 0.5, 1) mm size and (512, 512, 176) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from 4 to 0 (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to 
---

We used 2 acquisitions.
The acquisitions were taked one at the beginning and one at the end of the
scanning session [MPRAGE1-ODDBALL-STERNBERG-DTI-MPRAGE2] so after 1 hour
+/-.
The scanner perform a 'real time motion correction' over the scanning
session.
I use the 'mri_motion_correct' script to register and average the
acquisitions, and the 'talairach2' script to obtain the trasform.xfm.
Then I use the GUI for the -stage 1 (process volume) and -stage 2 (create
surface).
I attach an example of the segmentation.

- Original Message -
From: "Bruce Fischl" <[EMAIL PROTECTED]>
To: "F.Musso" <[EMAIL PROTECTED]>
Cc: <[EMAIL PROTECTED]>
Sent: Friday, September 17, 2004 4:08 AM
Subject: Re: bad segmentation [newbie]


> Hi Francesco,
>
> these look pretty bad. Can you describe the acquisitions? How many? Did
you
> motion correct and average them? What is the resolution? What field
> strength? What receive coil(s)?
>
> cheers,
> Bruce
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