It worked! DTIFit will now process the images. Thanks very much.
One last thing - just to clarify, a '1' in the bvecs file means sqrt
(2)? Why isn't it 1/sqrt(2)? When I produced these images I used
factors of 1/sqrt(2) in each direction, so the total magnitude would
always equal 1. For instance, in my 2nd volume (1 1 0) I multiplied
the total gradient by (1/sqrt(2)) in the x direction, and the same in
the y direction. Sorry if this is a stupid question, but how do I
tell FSL to use 1/sqrt(2) as a unit length?
Thanks
Patrick
On 15 Oct 2007, at 16:13, Tim Behrens wrote:
> 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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