Hi, Would someone kindly let me know that, in order to segment a tumor in brain, how/whether I can segment only one slice so it propagates through the adjacent slices and cover up the tumor? thanks, -S

On Tue, Jun 24, 2014 at 8:31 PM, Sam Raby rabysam28@gmail.com wrote:

Thanks. I would like to start learning and using freesurfer. I have a DICOM MRI of the brain which has a tumor in it. I would like to segment this tumor as automatically as possible. Can I segment only one slice so it propagates through the adjacent slices? Which tool in freesurfer do I need to use to achieve this?

Thanks, -S

On Tue, Jun 17, 2014 at 5:51 PM, Markus Gschwind < markus.gschwind@gmail.com> wrote:

...

Hi,

You can see here what to do: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall no 4., 5 and 6 especailly.

Cheers, M

2014-06-18 0:45 GMT+02:00 Sam Raby rabysam28@gmail.com:

...

I have downloaded the following file

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

and have extracted the contained files, and I was wondering where the binary file is so that I can open the freesurfer with? https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall

thanks -S

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Hi Sam, With the voxel edit tool in freeview, you can select the flood fill tool (paint bucket icon), and check the box labeled "Flood fill multiple slices at a time". You might have to play with the tolerance percentage to get a good rough-start segmentation of the tumor tissue. -Louis

On Wed, 25 Jun 2014, Bruce Fischl wrote:

Hi Sam

no, I don't think there is anything we have that will do tumor segmentation. I think there are some tools for manually segmenting structures and propagating segmentations from one slice to the next. Perhaps Ruopeng or some other power freeview user can comment?

cheers Bruce On Wed, 25 Jun 2014, Sam Raby wrote:

...

Hi, Would someone kindly let me know that, in order to segment a tumor in brain, how/whether I can segment only one slice so it propagates through the adjacent slices and cover up the tumor? thanks, -S

On Tue, Jun 24, 2014 at 8:31 PM, Sam Raby rabysam28@gmail.com wrote: Thanks. I would like to start learning and using freesurfer.  I have a DICOM MRI of the brain which has a tumor in it. I would like to segment this tumor as automatically as possible. Can I segment only one slice so it propagates through the adjacent slices? Which tool in freesurfer do I need to use to achieve this?

Thanks, -S

On Tue, Jun 17, 2014 at 5:51 PM, Markus Gschwind markus.gschwind@gmail.com wrote: Hi,  You can see here what to do: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall no 4., 5 and 6 especailly.

Cheers, M

2014-06-18 0:45 GMT+02:00 Sam Raby rabysam28@gmail.com: I have downloaded the following file freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

and have extracted the contained files, and I was wondering where the binary file is so that I can open the freesurfer with?

thanks -S

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.