Fsl_resample

[dilekozkan]

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]

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 1*1*1 flair image of the same patient to 3d 1*1*5 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! — Reply to this email directly, view it on GitHub <#33>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAIGPLSXRIA7ROBZHXS7OETV4EKWZANCNFSM6AAAAAAQCW6CAU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Best, John

[dilekozkan]

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]

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