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Subject:

Re: FDT questions

From:

Jon Clayden <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 8 Nov 2004 11:28:04 +0000

Content-Type:

text/plain

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Parts/Attachments

text/plain (153 lines)

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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