Ah, that highlighted the problem - somewhere along the line my bvals
and bvecs files have obviously got mangled since bedpost_datacheck
showed them as having too many lines. I've fixed this and dtifit now
seems to work fine. Sorry for the false alarm.
Thanks,
Jon
On Oct 26, 2004, at 16:57, Tim Behrens wrote:
> Hi Jon,
> Can you run bedpost_datacheck on the directory and email us the output.
> That should solve any easy problems.
>
> Thanks
>
> Tim
>
>
> -----------------------------------------------------------------------
> --------
> Tim Behrens
> Centre for Functional MRI of the Brain
> The John Radcliffe Hospital
> Headley Way Oxford OX3 9DU
> Oxford University
> Work 01865 222782
> Mobile 07980 884537
> -----------------------------------------------------------------------
> --------
>
> On Tue, 26 Oct 2004, Jon Clayden wrote:
>
>> Hi,
>>
>> I'm running FSL 3.2 on MacOS X.3.5, and I'm having trouble with
>> dtifit.
>> The directory with the files in looks like this:
>>
>> total 328784
>> -rw-r--r-- 1 jon jon 364 26 Oct 15:44 bvals
>> -rw-r--r-- 1 jon jon 2370 26 Oct 15:59 bvecs
>> -rw-r--r-- 1 jon jon 348 26 Oct 15:58 data.hdr
>> -rw-r--r-- 1 jon jon 81788928 26 Oct 15:58 data.img
>> -rw-r--r-- 1 jon jon 10010 26 Oct 15:58 data_ec.ecclog
>> -rw-r--r-- 1 jon jon 348 26 Oct 15:58 data_ec.hdr
>> -rw-r--r-- 1 jon jon 81788928 26 Oct 15:58 data_ec.img
>> -rw-r----- 1 jon jon 348 26 Oct 15:40 fT2W_av.hdr
>> -rw-r----- 1 jon jon 1572864 26 Oct 15:40 fT2W_av.img
>> -rw-r--r-- 1 jon jon 348 26 Oct 16:06 nodif.hdr
>> -rw-r--r-- 1 jon jon 1572864 26 Oct 16:06 nodif.img
>> -rw-r--r-- 1 jon jon 348 26 Oct 16:06 nodif_mask.hdr
>> -rw-r--r-- 1 jon jon 1572864 26 Oct 16:06 nodif_mask.img
>>
>> where data_ec.* were produced by running eddy_correct on data.*, and
>> nodif* were produced by running bet on the fT2W_av.* files. When I try
>> to run dtifit, I get this error (last line):
>>
>> jon$ dtifit -k data_ec -o dti -m nodif_mask -r bvecs -b bvals -V
>> data file data_ec
>> mask file nodif_mask
>> bvecs bvecs
>> bvals bvals
>> reading data
>> reading mask
>> ok
>> 0 128 0 128 0 48
>> setting up vols
>> copying input properties to output volumes
>> zeroing output volumes
>> ok
>> Forming A matrix
>> Abort trap
>>
>> and then it immediately quits. Can anyone shed any light on why this
>> may be happening?
>>
>> Thanks,
>> Jon Clayden
>>
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