In the morning things go better: when I used only img and hdr, eddy correct
run without errors and I can view it in fslview. The rest in progress...
Thanks for all help!
Aga
On 12.06.2007 18:36 Uhr, "Matt" <[log in to unmask]> wrote:
> How are you running MRIConvert? I suggest you run it with a commandline
> like this (for the windows version):
>
> mcverter /o .\ /f fsl /x /d /n FolderWithDICOMs/ and it should only give you
> one filetype (nii) that works properly with FSL.
>
> You should run something like:
>
> avwroi data nodif 0 1
> bet nodif nodif_brain -m -f .2
>
> to get the brain only mask.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Agnieszka Burzynska
> Sent: Tuesday, June 12, 2007 12:11 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Multiple files
>
> Thanks!
> Do you mean to have either .nii only or .hdr+.img? If so, now I get (with
> nii only): This program has not been compiled for this data type. also: bad
> header info.
> Perhaps i select something wrong: while selecting input file, I go to
> subjects´s folder and select .nii file of the DW sequence. Is it ok?
>
> Thanks,
> Aga
>
>
>
> On 12.06.2007 17:23 Uhr, "Matt" <[log in to unmask]> wrote:
>
>> Hi,
>>
>> Delete either the .nii or the .hdr & .img as these are the multiple files
>> (you only need one of the two).
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>> Of Aga Burzynska
>> Sent: Tuesday, June 12, 2007 11:11 AM
>> To: [log in to unmask]
>> Subject: [FSL] Multiple files
>>
>> Dear all,
>> Please forgive me such basic question, but I am just starting my work with
>> FSL and FDT.
>>
>> After MRIconvert (dicoms to FSL nifti 4D) of my DW raw data, I got .nii,
>> .img .hdr, bvecs and bvals, as expected. However, whatever I try to do
> with
>> FSL, I get the warning: Multiple image files detected. Is there anything
>> wrong with my DISH organization?
>>
>> I guess to get nodif_brain_mask I need to run BET...but this also
> complains.
>>
>> If you have any sources that would help me to solve such simple problems
>> without asking you, I will be very grateful.
>>
>> I will be grateful for any advice,
>>
>> Aga (PhD candidate)
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