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Hi expert, I found an issue when I do skull stripping. I used the following command line. recon-all \ -skullstrip \ -s fs_output \ -clean-bm \ -wsthresh 100 But, I found too much brain tissue has been removed, particularly for the visual and motor cortex, please see below.
Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include more brain tissues. Looking forward to your reply. Thanks. Best, Cain
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The image does not look very good. It looks very washed out (low contrast). Which volume is that?
On 8/5/2023 9:57 AM, DS wrote:
External Email - Use Caution
Hi expert, I found an issue when I do skull stripping. I used the following command line. recon-all \ -skullstrip \ -s fs_output \ -clean-bm \ -wsthresh 100 But, I found too much brain tissue has been removed, particularly for the visual and motor cortex, please see below.
Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include more brain tissues. Looking forward to your reply. Thanks. Best, Cain
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Hi expert, Thanks for your reply. Here is the raw T1.nii that I input. So, we can see the contrast is not that bad. But the image contrast of brainmask.mgz (recon-all output) seems low. I am not sure why it becomes low contrast in brainmask.mgz.
At 2023-08-07 21:09:15, "Douglas N. Greve" dgreve@mgh.harvard.edu wrote:
External Email - Use Caution
The image does not look very good. It looks very washed out (low contrast). Which volume is that?
On 8/5/2023 9:57 AM, DS wrote:
External Email - Use Caution
Hi expert, I found an issue when I do skull stripping. I used the following command line. recon-all \ -skullstrip \ -s fs_output \ -clean-bm \ -wsthresh 100 But, I found too much brain tissue has been removed, particularly for the visual and motor cortex, please see below.
Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include more brain tissues. Looking forward to your reply. Thanks. Best, Cain
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