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open-discussion > preprocessing of fMRI data in fsl
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Oct 26, 2021 01:10 PM | fereshte hoseinian
preprocessing of fMRI data in fsl
Hello everyone
I hope you are doing well.when I preprocess my
data(with fsl software) and then fit the model on it(with R
software), as result there is a ring around the brainI think the
problem is in preprocessing stepwould you please help me?I attached
a sample of my resultThank you for your time and consideration in
advance.All the best,
Fereshte
Oct 26, 2021 08:10 PM | Surendra Maharjan
RE: preprocessing of fMRI data in fsl
Hello,
Would you find posting a screenshot of your image?
Suren
Would you find posting a screenshot of your image?
Suren
Oct 27, 2021 11:10 AM | fereshte hoseinian
RE: preprocessing of fMRI data in fsl
Thank you for your attention
Oct 27, 2021 09:10 PM | fereshte hoseinian
RE: preprocessing of fMRI data in fsl
Originally posted by fereshte hoseinian:
Hello everyone
I hope you are doing well.when I preprocess my
data(with fsl software) and then fit the model on it(with R
software), as result there is a ring around the brainI think the
problem is in preprocessing stepwould you please help me?I attached
a sample of my resultThank you for your time and consideration in
advance.All the best,
Fereshte
Oct 28, 2021 01:10 PM | Yunior Cabrales - Biomedical Research and Innovation institute of Cadiz
RE: preprocessing of fMRI data in fsl
Dear fereshte,
I was looking to the .pdf file you have shared but unfortunately its resolution is too poor. Could you please load your data into fsleyes and then send a screenshot? I am not quite sure what you mean about a ring around the brain. If you refer to the white pixels it seems like the skull stripping was not very good and what you see is just cerebrospinal fluid. This is just my guess about this low-resolution image. As I mentioned before it would be better to see a good quality image before.
My advice: you should first check your fsl-preprocessed data with fsleyes or any other mri-specialized visualization software before analyzing your data with R or any other statistical-oriented package.
Best
Yunior
I was looking to the .pdf file you have shared but unfortunately its resolution is too poor. Could you please load your data into fsleyes and then send a screenshot? I am not quite sure what you mean about a ring around the brain. If you refer to the white pixels it seems like the skull stripping was not very good and what you see is just cerebrospinal fluid. This is just my guess about this low-resolution image. As I mentioned before it would be better to see a good quality image before.
My advice: you should first check your fsl-preprocessed data with fsleyes or any other mri-specialized visualization software before analyzing your data with R or any other statistical-oriented package.
Best
Yunior
Oct 28, 2021 02:10 PM | fereshte hoseinian
RE: preprocessing of fMRI data in fsl
I attached a screenshot of my data from fsleyes,
Oct 28, 2021 06:10 PM | Surendra Maharjan
RE: preprocessing of fMRI data in fsl
Hello Fereshte,
The contrast can be changed after processing. Would you mind watching Andrew Jahn videos on fMRI data processing? He has explained this very well.
Other than that, you can change threshold in bet if skull stripping is not adequate.
Many Thanks,
Suren
The contrast can be changed after processing. Would you mind watching Andrew Jahn videos on fMRI data processing? He has explained this very well.
Other than that, you can change threshold in bet if skull stripping is not adequate.
Many Thanks,
Suren