search

ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

remove islands #267

Closed 1alebra2 closed 4 years ago

1alebra2 commented 5 years ago

Hello everybody

Is there something like "remove islands" from a labelled image available? Or are there any workarounds?

any ideas are appreciated

alebra

dorianps commented 5 years ago

Define island, label or empty island?

On Mon, Apr 1, 2019 at 11:29 AM 1alebra2 notifications@github.com wrote:

Hello everybody

Is there something like "remove islands" from a labelled image available? Or are there any workarounds?

any ideas are appreciated

alebra

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267, or mute the thread https://github.com/notifications/unsubscribe-auth/AIqafUNqDyBXzSSzgan4SHD1nNaJr9Nhks5vciW7gaJpZM4cWA3P .

stnava commented 5 years ago

he may be talking about filling holes .... in which case iMath( img, "FillHoles" ) where you may need to some other steps like thresholding etc.

brian

On Mon, Apr 1, 2019 at 12:12 PM dorianps notifications@github.com wrote:

Define island, label or empty island?

On Mon, Apr 1, 2019 at 11:29 AM 1alebra2 notifications@github.com wrote:

Hello everybody

Is there something like "remove islands" from a labelled image available? Or are there any workarounds?

any ideas are appreciated

alebra

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267, or mute the thread < https://github.com/notifications/unsubscribe-auth/AIqafUNqDyBXzSSzgan4SHD1nNaJr9Nhks5vciW7gaJpZM4cWA3P

.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267#issuecomment-478643983, or mute the thread https://github.com/notifications/unsubscribe-auth/AATyflMtyRr0t0AgfNuj1lu3bkdPaNVWks5vci_RgaJpZM4cWA3P .

1alebra2 commented 5 years ago

I meant how an island of a label of a specific size.

Am 01.04.2019 um 18:12 schrieb dorianps notifications@github.com:

Define island, label or empty island?

On Mon, Apr 1, 2019 at 11:29 AM 1alebra2 notifications@github.com wrote:

Hello everybody

Is there something like "remove islands" from a labelled image available? Or are there any workarounds?

any ideas are appreciated

alebra

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267, or mute the thread

https://github.com/notifications/unsubscribe-auth/AIqafUNqDyBXzSSzgan4SHD1nNaJr9Nhks5vciW7gaJpZM4cWA3P .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

muschellij2 commented 5 years ago

see ?labelClusters John

On Mon, Apr 1, 2019 at 2:36 PM 1alebra2 notifications@github.com wrote:

I meant how an island of a label of a specific size.

Am 01.04.2019 um 18:12 schrieb dorianps notifications@github.com:

Define island, label or empty island?

On Mon, Apr 1, 2019 at 11:29 AM 1alebra2 notifications@github.com wrote:

Hello everybody

Is there something like "remove islands" from a labelled image available? Or are there any workarounds?

any ideas are appreciated

alebra

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267, or mute the thread

< https://github.com/notifications/unsubscribe-auth/AIqafUNqDyBXzSSzgan4SHD1nNaJr9Nhks5vciW7gaJpZM4cWA3P

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267#issuecomment-478694445, or mute the thread https://github.com/notifications/unsubscribe-auth/ABBnrjih1d6aQIkBpkD7-tH1MzvftVd8ks5vclGTgaJpZM4cWA3P .

dorianps commented 5 years ago

See here how I do it in a couple of lines, labelClusters with a threshold can do it, then you multiply the binarized result with your original label image to get rid of the small clisters: https://github.com/dorianps/LESYMAP/blob/master/R/lsm_sccan.R#L233-L234

On Mon, Apr 1, 2019 at 2:43 PM John Muschelli notifications@github.com wrote:

see ?labelClusters John

On Mon, Apr 1, 2019 at 2:36 PM 1alebra2 notifications@github.com wrote:

I meant how an island of a label of a specific size.

Am 01.04.2019 um 18:12 schrieb dorianps notifications@github.com:

Define island, label or empty island?

On Mon, Apr 1, 2019 at 11:29 AM 1alebra2 notifications@github.com wrote:

Hello everybody

Is there something like "remove islands" from a labelled image available? Or are there any workarounds?

any ideas are appreciated

alebra

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267, or mute the thread

<

https://github.com/notifications/unsubscribe-auth/AIqafUNqDyBXzSSzgan4SHD1nNaJr9Nhks5vciW7gaJpZM4cWA3P

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267#issuecomment-478694445, or mute the thread < https://github.com/notifications/unsubscribe-auth/ABBnrjih1d6aQIkBpkD7-tH1MzvftVd8ks5vclGTgaJpZM4cWA3P

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/ANTsX/ANTsR/issues/267#issuecomment-478697272, or mute the thread https://github.com/notifications/unsubscribe-auth/AIqafZoduHvTY-uh6JCgeTr5_dJ3IDr1ks5vclNYgaJpZM4cWA3P .