/Applications/fsl/bin/flirt -in
/Users/IMAC/Desktop/Nifti/itamar/dti_FA.nii.gz -ref
/Users/IMAC/Desktop/Nifti/itamar/newmprage_brain.nii.gz -out
/Users/IMAC/Desktop/a -omat /Users/IMAC/Desktop/a.mat -bins 256 -cost
corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6 -interp
trilinear
/Applications/fsl/bin/flirt -in
/Users/IMAC/Desktop/Nifti/itamar/newmprage-mask.nii.gz -applyxfm -init
/Applications/fsl/etc/flirtsch/ident.mat -out /Users/IMAC/Desktop/b
-paddingsize 0.0 -interp trilinear -ref
/Users/IMAC/Desktop/Nifti/itamar/dti_FA.nii.gz
I am using the FLIRT gui but here are the commands that print out. I have
checked the orientations and they are all in radiological orientation. In
this particular case the CC ROI that I created in T1 space appears directly
above the CC in diffusion space. So it is only off in terms of where it
should be in the superior-inferior plane but is dead on in terms of the
other 2 planes. Thanks again.
On Mon, 7 Apr 2008 08:25:01 +0100, Mark Jenkinson <[log in to unmask]> wrote:
>Hi,
>
>We need more information than this to diagnose the error.
>Can you send us the exact fsl command-lines that you are running?
>
>And also check if all your images are in "radiological" orientation
>as determined by fslorient. This can cause problems if you have
>a mix of "radiological" and "neurological".
>
>All the best,
> Mark
>
>
>On 7 Apr 2008, at 03:03, Ravi Shetty wrote:
>
>> Hi I have been using FLIRT to register my T1 and DTI images to each
>> other but keep running into
>> problems. The registered images produced are always very close to
>> what they should be when I
>> overlay them onto the T1 image. The problem I have is the matrixes
>> don't always reflect the
>> registration image. I create a CC ROI mask on the T1 image/
>> registered image and use the matrix I
>> produced to convert it back into difusion space. Now when I do this
>> with some subjects the ROI will
>> be spot on the CC and for others it will be off somewhere in the
>> cortex or even just into the black
>> void. I can't seem to find any rhyme or reason for this and the
>> variation of how off the matrix is does
>> not seem to be consistent, any help figuring this out would be
>> appreciated. Thanks.
>>
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