Hi Peter,
as far as I can see your bvals and bvecs files contain some non-ascii
entries. If you remove those, it should resolve the problem. Just open the
files with a txt editor and make sure you leave a single space between
consecutive numbers of the same line.
Cheers,
Stam
----- Original Message -----
From: "Tuo Peter Li" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Thursday, July 22, 2010 6:03 PM
Subject: [FSL] Problem running bedpostx or dtifit
Hi,
Bedpostx and dtifit report errors when I try to use them (I posted this
problem as a reply to the post on "ProbtrackX error," this error seems
different from that one, so I have started a separate post for this error.
Please pardon the duplicate post of the same problem).
The data looks like so:
bedpostx_datacheck ./
.//data
data_type INT16
dim1 128
dim2 128
dim3 40
dim4 140
datatype 4
pixdim1 0.2339999974
pixdim2 0.2343750000
pixdim3 0.5000000000
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
.//nodif_brain_mask
data_type INT16
dim1 128
dim2 128
dim3 40
dim4 1
datatype 4
pixdim1 0.2339999974
pixdim2 0.2343750000
pixdim3 0.5000000000
pixdim4 0.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in .//bvals
1
num words in .//bvals
140
num lines in .//bvecs
3
num words in .//bvecs
420
---------------------------
Bedpostx finishes prematurely as so:
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
Queuing post processing stage
Done!
All of the bedpostx.e1617.* files have the following error message:
An exception has been thrown
Logic error:- detected by Newmat: index error: requested indices = 3, 1
MatrixType = Rect # Rows = 2; # Cols = 140
--------------------------
Running dtifit displays the following message:
dtifit -k data -o dti_fdt -m nodif_brain_mask.nii -r bvecs -b
bvals --verbose
data file data
mask file nodif_brain_mask.nii
bvecs bvecs
bvals bvals
terminate called after throwing an instance of 'NEWMAT::IndexException'
Aborted
---------------------------
Files bvecs and bvals contain no funny non-asci symbols.
Neither data nor the mask has been upsampled or downsampled.
---------------------
Any ideas?
Regards,
Peter
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