Error output of fa_in_wm.csv

SCT
1

Hello SCT team,

I completed all the analysis and output the corresponding result file according to the specific steps on the website. After extracting the specific fa and ad values, I found that the final result was blank. I am sure that I have completed all steps correctly and checked the output of each step. I attach my results here
Uploading: dti_AD.nii.gz…
Uploading: dti_FA.nii.gz…
ad_in_wm.csv (227 Bytes)
fa_in_wm.csv (227 Bytes)

2

Hi @Shy,

I’m sorry to hear that you are experiencing difficulties. I would be happy to help. :slightly_smiling_face:

Could you please link to the exact commands that you were following?

Also:

It looks like your post may have been submitted while these files were being uploaded, so the files are inaccessible.

Could you please re-upload them?

Thank you kindly,
Joshua

3

Thanks for your reply. I have uploaded the relevant files again.
ad_in_wm.csv (227 Bytes)
fa_in_wm.csv (227 Bytes)
dti_AD.nii.gz (3.8 MB)
dti_FA.nii.gz (3.2 MB)

4

This txt file is all the commands I used with SCT. But about the warp_ dmri2template.nii.gz and the war_ template2dmri.nii.gz file, I downloaded these two files from the website (spinalcordtoolbox. com). I don’t know if this is the problem. I don’t know how to export these two files or whether they are universal. So I temporarily borrowed these two files downloaded from the website. The picture shows where I downloaded these two files.
output.txt (90.1 KB)
截屏2023-02-08 17.13.41.pdf (329.3 KB)

5

Thank you very much for the detailed reply.

Looking at your output.txt, it looks like you have the dMRI files already.

So, perhaps you mean that you re-used the following T2s files instead?

                        -initwarp ../t2s/warp_template2t2s.nii.gz \
                        -initwarpinv ../t2s/warp_template2t2s.nii.gz\

This is the problem. The files that are provided on spinalcordtoolbox.com are just example files. They are generated using an example dataset. They should not be mixed with your own personal data – they should only be used for testing out the commands.

So, you should be generating your own copies of warp_template2t2s.nii.gz and warp_template2t2s.nii.gz. (This requires having images in a separate high-resolution contrast (e.g. T1, T2, T2*) for the same subject, then following the steps in the Registration to Template tutorial.)

If you don’t have a separate contrast, and only have the dMRI files, then please let us know. We will try to help you find a way to compute metrics using only dMRI files. (See: this GitHub issue for more details.)

Kind regards,
Joshua

1 Like
6

Thanks very much for your reply. I think I should study it carefully on the website first, and thank you again for your reply!