PS -
> 0 1 0 1 0 1 -1
> 0 1 1 0 1 -1 0
> 0 0 1 1 -1 0 1
>
> i.e. the gradients directions have been normalized to unit length,
These are not unit length. They have a length of sqrt(2)
This does not matter for the new version of FDT, but probably does
matter for the old version you are working with
T
On 15 Oct 2007, at 15:53, Patrick Hales wrote:
> Hi
>
> Thanks again for the help. I've tried running bedpost_datacheck on
> my data (after renaming everything to the appropriate filenames).
> The output I get is:
>
> bedpost_data/data
> data_type INT16
> dim1 128
> dim2 128
> dim3 7
> dim4 1
> datatype 4
> pixdim1 0.2343750000
> pixdim2 0.2343750000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> cal_max 25500.0000
> cal_min 40.0000
> file_type NIFTI-1+
>
> bedpost_data/nodif does not exist
> bedpost_data/nodif_brain_mask
> data_type INT16
> dim1 128
> dim2 128
> dim3 7
> dim4 1
> datatype 4
> pixdim1 0.2343750000
> pixdim2 0.2343750000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> cal_max 4.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> num lines in bedpost_data/bvals
> 1
> num words in bedpost_data/bvals
> 7
> num lines in bedpost_data/bvecs
> 3
> num words in bedpost_data/bvecs
> 21
> number of elements in bvals is not equal to number of vols in data
> number of elements per line in bvecs is not equal to number of vols
> in data
>
> I don't understand what's wrong with my bvals and bvecs files. My
> 'data' file should now be made up of 7 volumes, the 1st with b=0
> and the other 6 with diffusion weighting in various directions. My
> bvals file looks like this:
>
> 0 1025 1048 826 1003 582 826
>
> and my bvecs file looks like this:
>
> 0 1 0 1 0 1 -1
> 0 1 1 0 1 -1 0
> 0 0 1 1 -1 0 1
>
> i.e. the gradients directions have been normalized to unit length,
> and the vectors run in columns. Could you tell me what I'm doing
> wrong with these files? - I've read the help and it sounds like I
> have set them up correctly, but I'm obviously doing something wrong.
>
> Thanks very much
>
> Patrick
>
>
>
>
>
>
> On 15 Oct 2007, at 14:28, Tim Behrens wrote:
>
>> Although - if you have the old version of FSL, it will be called
>> bedpost_datacheck!
>> T
>> On 15 Oct 2007, at 13:00, Matt Glasser wrote:
>>
>>> Hi,
>>>
>>> Fslmerge is in the latest version of FSL whereas avwmerge is in
>>> earlier
>>> versions. You could navigate to the data directory with the
>>> commandline and
>>> try running bedpostx_datacheck and post that output here.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>> On Behalf
>>> Of Patrick Hales
>>> Sent: Monday, October 15, 2007 6:36 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] Problem with DTIFit
>>>
>>> Hi
>>>
>>> Thanks for that. The command 'fslmerge' isn't recognized for some
>>> reason, however, I have been able to make my 4D data file using
>>> 'avwmerge' instead. Unfortunately, when I try to process the data in
>>> DTIFit, I now get the error message: "Error: child killed: bus
>>> error". Would you be able to tell me how to fix this?
>>>
>>> Thanks very much for your help
>>>
>>> Patrick
>>>
>>>
>>>
>>>
>>> On 15 Oct 2007, at 11:14, Tim Behrens wrote:
>>>
>>>> You need to merge your data from different diffusion directions
>>>> into a single 4D nifti file - you can use fslmerge to do this.
>>>>
>>>> T
>>>> On 15 Oct 2007, at 09:52, Patrick Hales wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> This is the first time I have tried using FSL, and I am trying to
>>>>> get the DTIFit program to work. I have
>>>>> a series of diffusion weighted images, each of which are stored as
>>>>> individual fid files (created using
>>>>> Varian's VnmrJ software). There are seven images in total, one
>>>>> with b=0 and 6 with diffusion
>>>>> gradients applied in non co-linear directions. I have converted
>>>>> each of these into Nifti format, and
>>>>> stored them all in a directory. I used FSLview to create my binary
>>>>> mask, and have created text files
>>>>> with my gradient directions (all normalized to unit length), and
>>>>> my b-values (in units of s/mm2). In
>>>>> the DTIFit program, I have selected 'specify input files
>>>>> manually', and supplied it with the directory
>>>>> containing my nifti files, and the filenames of my gradients
>>>>> and b-
>>>>> values text files.
>>>>>
>>>>> When I press 'go', I get a number of error messages, such as:
>>>>> 'ERROR: nifti_image_read(....directory
>>>>> name....)can't open header file', 'ERROR: nifti_image_open
>>>>> (...):bad header info', 'Error: failed to open
>>>>> file', etc. I get the same errors when I try it with analyze
>>>>> files.
>>>>>
>>>>> Would you be able to tell me what I'm doing wrong? Thanks very
>>>>> much
>>>>>
>>>>> Patrick Hales
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