Hi,
I have a couple of questions that are bothering me and don't seem to be
answered by the FAQ.
First, I've noticed that running avwhd on some of the Analyze files
generated by various stages of the FDT pipeline produces a seemingly
arbitrary mixture of positive and negative "pixdim1" values. (See, for
example, the bedpost_datacheck output below.) Is this expected; and if
so, what is happening? When I overlay output from probtrack with an FA
map from the same data the tractography results look rather unlikely in
parts, occasionally straying into CSF, so I wondered if one of the
images might be back-to-front with respect to the other.
Secondly, when I run bedpost it processes the data for about 12 hours,
which seems suspiciously short considering the spec of the box it's
running on (Red Hat 9 derivative, 2GHz or so, 512Mb RAM), and then
finishes with output like the following:
[...]
40 slices processed
41 slices processed
41 slices processed
42 slices processed
43 slices processed
44 slices processed
45 slices processed
Merging outputs into 4D files
DONE
/disk/home/cornell/s0343526/fsl/bin/bedpost: line 294: syntax error:
unexpected end of file
Should it be finishing at this point, or is something really wrong?
Thanks,
Jon
bedpost_datacheck output:
./data
dim1 128
dim2 128
dim3 48
dim4 52
datatype 4
pixdim1 -1.7187500000
pixdim2 1.7187500000
pixdim3 2.7999999523
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
glmax 0
glmin 0
origin1 0
origin2 0
origin3 0
file_type ANALYZE-7.5
./nodif
dim1 128
dim2 128
dim3 48
dim4 1
datatype 4
pixdim1 1.7187500000
pixdim2 1.7187500000
pixdim3 2.7999999523
pixdim4 1.0000000000
cal_max 1385.0000
cal_min 0.0000
glmax 0
glmin 0
origin1 0
origin2 0
origin3 0
file_type ANALYZE-7.5
./nodif_brain_mask
dim1 128
dim2 128
dim3 48
dim4 1
datatype 4
pixdim1 -1.7187500000
pixdim2 1.7187500000
pixdim3 2.7999999523
pixdim4 1.0000000000
cal_max 1.0000
cal_min 0.0000
glmax 0
glmin 0
origin1 0
origin2 0
origin3 0
file_type ANALYZE-7.5
num lines in ./bvals
1
num words in ./bvals
52
num lines in ./bvecs
3
num words in ./bvecs
156
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