Hi Stephen,
The platform is Red Hat Linux 9 (x86). The output data look plausible,
except for the fact that superimposing them onto an FA map generated by
dtifit sometimes shows bright areas in CSF, as I mentioned. Is it valid
to overlay these two images, and if not, what should I be putting
"under" the probtrack results in fslview?
Thanks,
Jon
On 6 Nov 2004, at 10:04, Stephen Smith wrote:
> Hi Jon.
>
> Don't worry about the -ve pixdims - that's something we'll tidy up in
> a future release but they should always not make a difference anyway.
>
> The analysis could well be that quick if your data is lower
> resolution/field-of-view than we used for the example timings in the
> manual.
>
> The error message on completion looks odd, particularly as the bedpost
> script is only 293 lines long. What platform are you using? It does
> look
> as if it probably did finish fine - I assume that the output data
> looked
> ok.
>
> Cheers.
>
>
>
> On Wed, 3 Nov 2004, Jon Clayden wrote:
>
>> 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
>>
>
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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