Hi George,
I was getting similar errors when I switched from FSL 2.2 to 2.3. My
problem was due to setting the origin at the anterior commissure following
the instructions at MRIcro for reorienting scans. When I reset the origin
to 0, 0, 0, the new SIENAX worked fine.
Hope this helps,
Yossi
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On Behalf Of
George Thomas
Sent: Monday, May 09, 2005 3:37 PM
To: [log in to unmask]
Subject: [FSL] SIENAX errors
I am trying to perform SIENAX, and the results are consistently very
wrong. Specifically, I am using a segmentation threshhold setting of
0.3 (-f0.3), which I have done without problem in the past. The data
from which my output is derived (the .hdr and .img files) were
previously and successfully processed with SIENAX at the default
segmentation threshold. Does SIENAX alter data (the .hdr and .img
files) during calculation? Do I need to use 'fresh' data to get more
realistic results? Below is a typical output-you can see that the
calculated volumes are impossibly small:
SIENA - Structural Image Evaluation, using Normalisation, of Atrophy
part of FSL www.fmrib.ox.ac.uk/fsl
running cross-sectional atrophy measurement: sienax version 2.3
sienax XXX -d -f0.3
---------- extract brain --------------------------------------------
---------- register to talairach space using brain and skull --------
(do not worry about histogram warnings)
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
VSCALING 1.4349560517
---------- mask with talairach mask ---------------------------------
---------- segment tissue into types --------------------------------
Unknow argument: -f
FAST - FMRIB's Automated Segmentation Tool
FAST Version 3.5
Usage: fast [-options] imagefile
options:
-t<n>: input image type. 1-T1, 2-T2, 3-PD (default T1)
-c <n>: number of classes (default 3)
-a: use apriori probability maps (for initialisation only)
-A: use apriori probability maps (for initialisation and for
posteriors)
-od <base>: output basename (default <input>)
-os: output segmentation with one class per image
-op: output probability maps (one for each class)
-or: output restored image
-ob: output bias correction field
-n: do not output segmentation
-m <file>: use file with starting values for the mean of each
tissue
-2: 2D segmentation (only for 3D images)
-i <n>: number of iterations (default 8)
-l <n>: iterations for bias correction field smoothing (default
100)
-p: disable automatic parameter updating
-b <v>: MRF neighbourhood beta value (default 0.3)
-oba <n>: output dilated bias correction field (n iterations)
-e: enable partial volume classification
-ov: output partial volume images (one for each class)
--b <v>: MRF beta value for PVE classification (default 1.5)
--p: disable parameter updating during PVE classification
-v<n>: verbose level (0-5; default 1)
---------- convert brain volume into normalised volume --------------
GREY 1.4349560517
WHITE 1.4349560517
BRAIN 2.8699121034
gpt
George Patrick Thomas, Jr.
SOM08
University of Kansas Medical Center
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