Dear Tim and FSL experts,
Could I ask a following question? Did anyone know how to transorm the raw
b-vectors into new b-vectors use the transformation matrix ? Is there any
script to do it ?
sincerley
kl chen
On Tue, 2 Jan 2007 09:30:40 +0000, Tim Behrens <[log in to unmask]>
wrote:
>Hi - I don't think you can estimate, and apply a transform to a 4D
>image simultaneously.
>
>I think you need to do the following:
>
>1) Register the b=0 image to the MNI template using FLIRT and save
>the transformation matrix.
>2) Apply this transformation matrix to the full 4D volume (using
>ApplyXFM)
>
>This will then save all of your volumes in the output.
>
>Remember that you will have to rotate the b-vectors as well if you
>want your fitted diffusion tensors to make sense.
>
>T
>
>On 2 Jan 2007, at 09:08, Anna Rotarska-Jagiela wrote:
>
>> Dear FSL expersts,
>> I’m trying to align my raw DTI data using FLIRT and write it out in
>> Analyze
>> format.
>> Here is what I did: I created a single Analyze file of raw DTI data (7
>> volumes, 6 directions + b0), did EPI distortion correction and
>> saved it
>> again as a single Analyze file. Then I opened FLIRT window,
>> selected input
>> image (a single Analyze EPI-corrected file with 7 volumes), named
>> output
>> image. I left all the other setting at default, including the
>> reference
>> image, i.e. MNI template. I clicked on go and checked the results
>> in MRIcro.
>> Here is the problem: The alignment worked fine, but the volumes got
>> lost. I
>> can only open the first, b0 volume. MRIcro doesn’t ask anymore
>> which volume
>> it should show (1 through 7) like it did with EPI-corrected image.
>> It only
>> recognizes the first one.
>> Here is the question: What did I do wrong? How do I align all 7
>> volumes and
>> save them back to a single Analyze file?
>> I would appreciate your help.
>> Thank you.
>>
>> Anna
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