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
