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muschellij2 / fslr

FSL-R Interface package
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Fsl_resample #33

Open dilekozkan opened 2 years ago

dilekozkan commented 2 years ago

Hello, I want to convert the 3d 111 flair image of the same patient to 3d 115 flair. And I want it to be in the transversal plane. I opened applyxfm in the user interface in fsl.

I put the flair image of the patient with the voxel sizes I wanted as the reference volume. It only takes the patient's voxel dimensions, not the image content, am i right? If the image will register, it will be wrong..

And I clicked the identity matrix button as transformation matrix question. Is there anything wrong with all this? Please let me know.

By the way, i ran this command and it didnt work. flirt -in /ms/flairhigh.nii -ref /ms/flairhigh.nii -applyxfm -out /ms/out

The image came in sagittal, but the transverse plane I put in was (user interface option) Thanks in advance!

muschellij2 commented 2 years ago

Are you sure about the image orientations of both images?

On Thu, Sep 1, 2022 at 5:02 PM Dilek Ozkan @.***> wrote:

Hello, I want to convert the 3d 111 flair image of the same patient to 3d 115 flair. And I want it to be in the transversal plane. I opened applyxfm in the user interface in fsl.

I put the flair image of the patient with the voxel sizes I wanted as the reference volume. It only takes the patient's voxel dimensions, not the image content, am i right? If the image will register, it will be wrong..

And I clicked the identity matrix button as transformation matrix question. Is there anything wrong with all this? Please let me know.

By the way, i ran this command and it didnt work. flirt -in /ms/flairhigh.nii -ref /ms/flairhigh.nii -applyxfm -out /ms/out

The image came in sagittal, but the transverse plane I put in was (user interface option) Thanks in advance!

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dilekozkan commented 2 years ago

3d 111 images has not specific direction, i can see the different orientation. And the other reference was a different patient's transvers scan as the voxel size 1 1 5

dilekozkan commented 2 years ago

the output of the command: flirt -in /ms/flairhigh.nii -ref /ms/flairtransvers.nii -applyxfm -out /ms/out It is sagittal again not axial. but the reference is axial i added the output. outputfsl.zip

It is my input inputforfsl.zip

it is my reference (this is the 2d flair of another patient) referenceforfsl.zip