incomplete *_aligned_trilin.nii.gz

[snaillyd]

Hi mrDiffusion experts, We used following command lines to preprocess DTI data: dwParams = dtiInitParams('clobber',1,'phaseEncodeDir',2); dtiInit('path to DTI nifti','path to T1.nii.gz',dwParams);

The *_aligned_trilin.nii.gz file is incomplete with part of the frontal lobes cropped.

Can anyone help us solve this problem? Thanks!

[hejieshi]

Hi, Did you solve this problem? PS: I tried using Ants to calculate the affine transformation parameters, but the results were inconsistent with spm_coreg.

[garikoitz]

I remember having similar problemas in the past... Can you try first to convert all files to RAS and then run the same command?

On Tue, Oct 10, 2023 at 11:04 AM hejieshi @.***> wrote:

Hi, Did you solve this problem? PS: I tried using Ants to calculate the affine transformation parameters, but the results were inconsistent with spm_coreg. [image: image] https://user-images.githubusercontent.com/61490713/273840516-6caaa37f-4486-4f54-a820-e13bd1cea78c.png

— Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/345#issuecomment-1754770595, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCZAV7ITPGRQ3SEH5YGHBTX6UFTLAVCNFSM4T5VAWZ2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZVGQ3TOMBVHE2Q . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[hejieshi]

The result is like this. The B0 image was not properly aligned to the T1 image (misaligned), and the cerebellum has been cut off.

Thanks!

[garikoitz]

I cannot tell how good or bad is... I normally use ANTs, maybe you want to give it a try and compare

On Tue, Oct 10, 2023 at 12:20 PM hejieshi @.***> wrote:

The result is like this. [image: image] https://user-images.githubusercontent.com/61490713/273864381-5c467aa4-cf1b-4e93-aada-89f6bf4e5d60.png The B0 image was not properly aligned to the T1 image (misaligned), and the cerebellum has been cut off.

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/vistalab/vistasoft/issues/345#issuecomment-1754901701, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCZAV2OCP2KSNS4CCATLOTX6UOODAVCNFSM4T5VAWZ2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZVGQ4TAMJXGAYQ . You are receiving this because you commented.Message ID: @.***>

[hejieshi]

It appears that the issue is related to the resolution of my T1 image resolution(0.50.50.8) . My solution is to perform ACPC correction on the T1 image in advance and resample it to 111 resolution. Then, I use this resampled T1 image as the input for dtiInit. This way, the alignment output is correct. you can see the difference with pic above