Unable to generate qc report in html and cannot find the fsleyes report

SCT
1

Hello,
I just started learning to SC toolbox for my research and using Linux on windows 11. I am practicing on the course material provided by SC toolbox and unable to see the qc report in html when I am inputting the following command:

sct_propseg -i t2.nii.gz -c t2 -qc /home/pawan_0210/qc-singleSubj

I do see an html report generated at the end, but I am unable to open it in the browser.

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Also, fsleyes latest version is installed on my computer, but i don’t see qc reported generated for the fsleyes.
Please let me know how can I fix this issue.

Thank you,
Pawan

2

I was able to solve the issue.

Thank you,
Pawan

1 Like
3

Hi @pawan_sharma,

My apologies for the late reply, but I’m glad to hear that you were able to resolve this issue on your own.

Is there anything that we can make clearer in the course materials? (For example, a specific step or instruction to better explain how to open the reports?)

Kind regards,
Joshua

4

Hello @Joshua_Wang,
Thanks for getting back. I guess the instructions in the course material are pretty clear. It was a lack on my understanding of the Linux usage on windows.
Can i perform the atlas based analysis using T2 weighted images if I don’t have the T2* images? I tried running the sct_deepseg_gm on T2 data and the masking looks very bad. Please let me know. If required, I can pose this as a new question too.

Pawan

5
Minimized

Short answer: No, I don’t believe you can use sct_deepseg_gm on T2-weighted images.

Long answer: sct_deepseg_gm was developed using the “Spinal cord grey matter segmentation challenge” dataset.

image

As shown above in the sample images, the training dataset has:

  1. Clear differentiation between white and gray matter
  2. A consistent colour scheme (dark grey + light grey).

image

Unfortunately, to my knowledge, T2-weighted data does not meet these two criteria, which is why sct_deepseg_gm performs poorly on T2-weighted data.

@jcohenadad might be able to chime in with more specific knowledge about the typical characteristics of T2-weighted data, though, as he is more knowledgeable than I am on these matters.

Hope this helps,
Joshua

6

Please disregard my previous answer, as it was missing some information.

@jcohenadad will respond with updated information on how to proceed with processing T2-weighted data. :slight_smile:

7

@joshuacwnewton thank you for the useful context/information you provided, it helps to better understand the context.

@pawan_sharma thank you for reaching out to us. Yes, you can perform atlas-based analysis without T2*-weighted images. In fact, this is how most people do it (including our group). To do so, you just need to skip the section that related to the T2*-weighted data processing. In the example batch script, it corresponds to these lines. Note that in the example script, the lines are commented out, so this script effectively performs atlas-based analysis without the T2*-weighted scan.

Unrelated: I see that the title of this thread is “Unable to generate qc report in html and cannot find the fsleyes report”, which is unrelated to the discussion about the use of the T2*-weighted scan. In the future, can you please create a new thread with an explicit title that corresponds to your question? That way, other people will be able to more easily search for answers in the forum, based on the title of each discussion thread. Thank you for your understanding.

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Thank you for getting back to me. Really appreciate it.

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@jcohenadad Thank you for getting back to me. I still have some doubts. I will create a new thread and follow up on that.

Really appreciate your time.
Pawan

1 Like