Dear FSL team,
I have tried to use a BET skull image as an apriori image in
the FAST segmentation algorithm. There appears to be a problem with
locating a matrix file. Perhaps there are some assumptions about apriori
image files that are not clear to me. I hope you can advise how to
generate appropriate apriori images for FAST.
Thanks, in advance, Darren
Here is the command line & associated output:
fast -t 1 -c 1 -n -op -a
ptsdpet-c01/mri/analyze/c01_orig_axial_ras_bet_skull.img
ptsdpet-c01/mri/analyze/c01_orig_axial_ras.img
number of classes can only be between 2 and 6 and is set to
3
FAST - FMRIB's Automated Segmentation Tool Version
3.1
Image:
ptsdpet-c01/mri/analyze/c01_orig_axial_ras.img
T1-weighted image
Imagesize : 256 x 256 x 256
Pixelsize
: 1 x 1 x 1
registering the probability maps to the
image...
/usr/local/fsl/bin/flirt -omat
ptsdpet-c01/mri/analyze/c01_orig_axial_rasin2st.mat -in
ptsdpet-c01/mri/analyze/c01_orig_axial_ras.img -ref
/usr/local/fsl/etc/standard/avg152T1_brain.hdr
/usr/local/fsl/bin/convert_xfm
-matonly -inverse -omat ptsdpet-c01/mri/analyze/c01_orig_axial_rasst2in.mat
ptsdpet-c01/mri/analyze/c01_orig_axial_rasin2st.mat
Could not open matrix
file ptsdpet-c01/mri/analyze/c01_orig_axial_rasin2st.mat
Cannot read
input-matrix
/usr/local/fsl/bin/flirt -init
ptsdpet-c01/mri/analyze/c01_orig_axial_rasst2in.mat -applyxfm -o
ptsdpet-c01/mri/analyze/c01_orig_axial_rasgm.hdr -in
/usr/local/fsl/etc/standard/avg152T1_gray.hdr -ref
ptsdpet-c01/mri/analyze/c01_orig_axial_ras.img
/usr/local/fsl/bin/flirt -init
ptsdpet-c01/mri/analyze/c01_orig_axial_rasst2in.mat -applyxfm -o
ptsdpet-c01/mri/analyze/c01_orig_axial_raswm.hdr -in
/usr/local/fsl/etc/standard/avg152T1_white.hdr -ref
ptsdpet-c01/mri/analyze/c01_orig_axial_ras.img
/usr/local/fsl/bin/flirt -init
ptsdpet-c01/mri/analyze/c01_orig_axial_rasst2in.mat -applyxfm -o
ptsdpet-c01/mri/analyze/c01_orig_axial_rascsf.hdr -in
/usr/local/fsl/etc/standard/avg152T1_csf.hdr -ref
ptsdpet-c01/mri/analyze/c01_orig_axial_ras.img
ZAVWImage::Open: Warning,
ptsdpet-c01/mri/analyze/c01_orig_axial_rasgm.hdr -- Can not open header
file!
Can not read apriori GM probability image gray.tif
