I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated.
Thanks,
Katie
Hi Katie,
you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold
cheers Bruce
On Fri, 1 Jul 2011, Katie Bettencourt wrote:
I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks,
Katie
Hi Bruce,
That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation.
Katie
On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Katie,
you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold
cheers Bruce
On Fri, 1 Jul 2011, Katie Bettencourt wrote:
I'm trying to draw an ROI by selecting the center of activation for a
particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks,
Katie
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/**compliancelinehttp://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.
you can draw a boundary between them and also click "up to boundaries" or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation.
Katie
On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Katie,
you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold cheers BruceOn Fri, 1 Jul 2011, Katie Bettencourt wrote:
I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, KatieThe 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.
What do you mean by dilate it?
Katie
On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
you can draw a boundary between them and also click "up to boundaries" or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Hi Bruce,
That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation.
Katie
On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Katie,
you can use the custom fill tool in tksurfer for this. Display youractivation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold
cheers BruceOn Fri, 1 Jul 2011, Katie Bettencourt wrote:
I'm trying to draw an ROI by selecting the center of activation for aparticular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks,
KatieThe 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/**compliancelinehttp://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.
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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.
under tools->label in tksurfer (I think) there's an option to dilate or erode the boundary (expand or contract)
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
What do you mean by dilate it? Katie
On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can draw a boundary between them and also click "up to boundaries" or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation. Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Katie, you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie 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.
Ok, I see it. I'll see what I can do with this, but I guess that means there's no way to do it and enter an explicit number of voxels to select from that central point?
Katie
On Fri, Jul 1, 2011 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
under tools->label in tksurfer (I think) there's an option to dilate or erode the boundary (expand or contract)
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
What do you mean by dilate it?
Katie
On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can draw a boundary between them and also click "up to boundaries" or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that weare going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation.
Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Katie,
you can use the custom fill tool in tksurfer for this. Displayyour activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center of activationfor a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks,
Katie The information in this e-mail is intended only for the person towhom 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/**compliancelinehttp://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/**freesurferhttps://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/**compliancelinehttp://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.
not really On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Ok, I see it. I'll see what I can do with this, but I guess that means there's no way to do it and enter an explicit number of voxels to select from that central point? Katie
On Fri, Jul 1, 2011 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: under tools->label in tksurfer (I think) there's an option to dilate or erode the boundary (expand or contract)
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
What do you mean by dilate it? Katie On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: you can draw a boundary between them and also click "up to boundaries" or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: Hi Bruce, That's how I normally make my ROIs, but my boss is concerned that we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation. Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Katie, you can use the custom fill tool in tksurfer for this. Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie 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.
Ok, thanks!
Katie
On Fri, Jul 1, 2011 at 2:54 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
not really
On Fri, 1 Jul 2011, Katie Bettencourt wrote:
Ok, I see it. I'll see what I can do with this, but I guess that means
there's no way to do it and enter an explicit number of voxels to select from that central point? Katie
On Fri, Jul 1, 2011 at 2:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: under tools->label in tksurfer (I think) there's an option to dilate or erode the boundary (expand or contract)
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote:
What do you mean by dilate it? Katie On Fri, Jul 1, 2011 at 2:28 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: you can draw a boundary between them and also click "up to boundaries" or something like that. Or just click the center and dilate it a few times or some combination of thresholding and dilation. It's quite flexible
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: Hi Bruce, That's how I normally make my ROIs, but my boss is concernedthat we are going from one area to a nearby area that is also activated by this contrast, so she wants to restrict it by a certain number of voxels from the center of activation.
Katie On Fri, Jul 1, 2011 at 1:55 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Katie,
you can use the custom fill tool in tksurfer for this.Display your activation map at whatever threshold you want, then click in the middle of the blob you want to create an ROI for and do custom fill with "up to functional threshold". This will floodfill from that point outwards stopping when it reaches vertices that are below threshold
cheers Bruce On Fri, 1 Jul 2011, Katie Bettencourt wrote: I'm trying to draw an ROI by selecting the center ofactivation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks,
Katie The information in this e-mail is intended only for the personto 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/**compliancelinehttp://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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person towhom 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/**compliancelinehttp://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@nmr.mgh.harvard.edu
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