8000 prepare_microbleed_data command · Issue #3 · v-sundaresan/microbleed-detection · GitHub
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SolerseYSU opened this issue Nov 25, 2023 · 1 comment
Open

prepare_microbleed_data command #3

SolerseYSU opened this issue Nov 25, 2023 · 1 comment
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@SolerseYSU
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@v-sundaresan
Hello, I'm stuck on using your prepare_microbleed_data command.
Can you tell me how I'm supposed to specify the directories for the input images and output images by showing me a specific command example?
Also, how are we supposed to organize our data? should all of our .nii files be zipped in a .nii.gz format and then prepared through the command above?
Can anyone who succeeded in using this module help me?

Thank you for your great code btw.
@EllieMo
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EllieMo commented Oct 29, 2024 •
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I had similar issues with the prepare_microbleed_data command. I ended up going into the code to see what it does and then preprocessed my data myself. It seems to me that you only need ${outname}_preproc.nii.gz in your input folder for microbleednet to run.

> # REORIENTING FLAIR AND T1 IMAGES TO STD SPACE
> $FSLDIR/bin/fslreorient2std ${inpfile}.nii.gz ${TMPVISDIR}/INPUT.nii.gz
> 
> # PREPROCESSING OF FLAIR IMAGE
> $FSLDIR/bin/bet ${TMPVISDIR}/INPUT.nii.gz ${TMPVISDIR}/INPUT_brain.nii.gz
> $FSLDIR/bin/fast -B --nopve ${TMPVISDIR}/INPUT_brain.nii.gz
> ${FSLDIR}/bin/imcp ${TMPVISDIR}/INPUT_brain_restore.nii.gz ${outdir}/${outname}_preproc.nii.gz
>

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@EllieMo @SolerseYSU
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