I am sorry for my late reply.
>
> 1-1 I found that the iteration time and registration type in the advanced settings influence the registration results. By using an affine registration and manually adjusting the scaling, shearing, and rotation parameters, I managed to obtain an acceptable result after running registration several times. The z scaling factor matters a lot. Do you think the manual adjustment is proper and necessary to get good registration?
Yes, because there is likely a distortion in the DWI.
>
> 1-2 The slice orientation of DWI is sagittal while the orientation of T2W is axial in our data. Could it be this orientation difference that leads to poor registration?
Likely, if the orientation matrix is not properly recorded in the
NIFTI header or DICOM header
>
>
> 2-1 I downloaded the newest version of DSI Studio via 'dsi_studio_windows_64.zip'. However, the second problem still rises and the FA map seems to be almost "white" after opening the FIB file. I wondered if this results from the difference in the orientations between DWI and T2W sequences. Could I manually adjust the registration in [Step 3] after inserting the T2W images, rather than upsample the DWI data to T2W in [Step 2]?
It is likely to be a bug in DSI Studio, but I could not reproduce the
same problem at my side.
Could you send me your SRC file and T2W to fix the program?
>
> 2-2 By the way, I tried to output tensor matrix in [Step 2] by adding txx, txy, txz, tyy, tyz, tzz in the 'Other output metrics'. However, the FIB file still does not contain the metrics of tensor matrix. Could you please give me some advice on getting the tensor matrix?
>
Please specify "tensor" to get these metrics.
Best regards,
Frank
>
> Really appreciate your help. Look forward to your reply.
>
> Best regards,
> Shihan
> On Saturday, 7 August 2021 at 03:52:01 UTC+8 Frank Yeh wrote:
>>
>> Hi Shihan,
>>
>> It is likely that the DWI has a large distortion that causes misalignment, and there is not much we can do other than correcting the distortion using FSL TOPUP.
>>
>> The second problem. You may update to the most recent version of DSI Studio and generate a new FIB file to see if it works.
>>
>> Best regards,
>> Frank
>>
>> On Wed, Aug 4, 2021 at 11:35 PM Shihan <
mmass...@gmail.com> wrote:
>>>
>>> Hi Frank,
>>>
>>> Thank you for your software.
>>>
>>> I'm currently using DSI Studio for fibre tractography in skeletal muscles. I have two questions about the automatic registration from DTI to T2W images.
>>>
>>> 1. I tried to upsample the DTI to the T2W space by using [Step T2][Edit][Resample to T1W/T2W]. The T2W with nii format was imported as a reference. However, the registration only fits some slices, as shown below. The registration results were poor at the wrist(fig1) and elbow(fig3). I also tried to run affine registration rather than rigid body, but the result was also not very well. Could you give me some advice on the processing steps or recommend some other tools to perform the registration?
>>>
>>>
>>> 2. Another question is that if I performed [Rotate to T1W/T2W] in [Step T2], the output fib file seems to have wrong fa values as shown in fig4, compared with the fa values without the preprocessing (fig5). And in fig4 condition, fibers can hardly be tracked.
>>>
>>>
>>>
> To view this discussion on the web visit
https://groups.google.com/d/msgid/dsi-studio/6b066a17-9003-4701-9951-f5796f0dde4dn%40googlegroups.com.