registration command

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Mark Pinsk

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Jan 13, 2023, 9:28:30 PM1/13/23
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Hi Frank

I get very nice registration results using R2: Nonlinear Registration Toolbox GUI with the parameters in the screenshot below.

I try to automate this on the command-line, but I do not get the same result. The registration from the command-line is not quite as good and also less smoothed.

It appears there are parameters I need to set on command-line to match what I set in the GUI, but I don't know how to set them. Specifically: "Edge Matching", "Large Deform", "Correlation", "Smoothing", and "Speed".  I suspect those parameters are necessary to get the same result.

Can you let me know if and how to match the command line to what I have in the GUI below?

Here is my command so far:

        dsi_studio \
        --action=reg \
        --from=ses-03.gqi.fib.gz.dti_fa.nii.gz \
        --from2=ses-03.gqi.fib.gz.rd.nii.gz \
        --to=ses-01.gqi.fib.gz.dti_fa.nii.gz \
        --to2=ses-01.gqi.fib.gz.rd.nii.gz \
        --output=ses-03.gqi.fib.gz.dti_fa.nii.gz.wp.nii.gz \
        --output_warp=ses-01-mapping \
        --reg_type=1 \
        --normalize_signal=1 \
        --iteration=64 \
        --resolution=2 \
        --min_dimension=8


And here are the parameters in the GUI that work best for me.

Screenshot 2023-01-13 at 9.12.16 PM.png




Mark Pinsk

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Jan 19, 2023, 10:08:40 AM1/19/23
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I was able to use the GUI for all my subjects these past days, so all is good !   If there's a future possibility of making the reg action command-line with all the GUI options, that would be wonderful.   Thanks!  Mark

Fang-Cheng Yeh

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Jan 19, 2023, 8:34:26 PM1/19/23
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Sorry for missing this thread.

I will review code to figure out the difference and fix it.

I will also prepare a document about how to do it in command line.

Best regards
Frank

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Mark Pinsk

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Jan 23, 2023, 10:58:31 AM1/23/23
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Thanks Frank!  I look forward to that.

Fang-Cheng Yeh

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Feb 16, 2023, 12:30:41 PM2/16/23
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I updated DSI Studio to provide --large_deform=1 and --use_edge=1
The new build is undergoing at https://github.com/frankyeh/DSI-Studio/actions/runs/4196575548
Please update and see if it works for you.
Frank


Mark A. Pinsk

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Feb 16, 2023, 2:49:11 PM2/16/23
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Thanks, I’ll give it a try.   Is there a way to specify “Correlation”, “Smoothing”, and “Speed” ? 

 

What is “Speed” ?

 

 

 

 

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Fang-Cheng Yeh

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Feb 16, 2023, 3:03:47 PM2/16/23
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Sorry for missing these parameters. I modified DSI Studio to support the following:

--cost_function=cc
--speed=1.0
--smoothing=0.2


Mark Pinsk

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Feb 16, 2023, 3:34:45 PM2/16/23
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<thumbs up>

Mark Pinsk

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Feb 16, 2023, 8:55:36 PM2/16/23
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it works, thanks!
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