Re: [Freesurfer] adding insula voxels
Hi Adam, Well that is good to hear! So you are all set with this problem then? -Ani On Thu, 6 Nov 2014, Adam Mezher wrote: Hi Ani, I actually did end up fixing the insula mis-segmentation using either control points or WM edits for many subjects (I think the one I sent you too, not sure). However, I did notice that in some subjects, the edits will push the wm line out a little too much such that minor part of the medial insula will be labeled as WM instead of insula. It is pretty minor though so don’t think it is a big deal anyway. -Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] adding insula voxels
Hi Ani, I actually did end up fixing the insula mis-segmentation using either control points or WM edits for many subjects (I think the one I sent you too, not sure). However, I did notice that in some subjects, the edits will push the wm line out a little too much such that minor part of the medial insula will be labeled as WM instead of insula. It is pretty minor though so don’t think it is a big deal anyway. -Adam ___ 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.
Re: [Freesurfer] adding insula voxels
Hi Adam, I know in your past email you mentioned that you do not think control points could fix the situation, could you tell me why you think that? Have you tried adding some and it failed? I took a look at your data and the wm value seems pretty low (low 70-80s) around the area near where the surfaces cut off the insula. I would suggest putting a in a few control points and running the subject again. If this does not work, let us know and I can look into some other options. But if you can fix it in the surfaces first, it will push the gm line out and that area will get included in the aparc label later on. Right now it probably isn't being labeled because it isn't considered part of the cortex. -Ani On Thu, 30 Oct 2014, Adam Mezher wrote: I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks! ___ 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.
Re: [Freesurfer] adding insula voxels
I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it? Thanks!___ 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.
Re: [Freesurfer] adding insula voxels
Can you send us an image? > On Oct 30, 2014, at 7:48 PM, Adam Mezher wrote: > > > I believe it's in the surfaces. It is apparent when I load the lh.pial and > lh.white over the brainmask. > > thanks, > Adam > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ 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.
Re: [Freesurfer] adding insula voxels
I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam ___ 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.
Re: [Freesurfer] adding insula voxels
Hi Adam underestimated the insula in the aseg or in the surfaces? cheers Bruce On Wed, 29 Oct 2014, Adam Mezher wrote: Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go about editing them manually by adding the correct label to the empty voxels with the Edit Segmentation tool in tkmedit. Thank you, Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] adding insula voxels
Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go about editing them manually by adding the correct label to the empty voxels with the Edit Segmentation tool in tkmedit. Thank you, Adam ___ 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.
Re: [Freesurfer] adding insula voxels
Hi Adam sorry, I've lost the context for this. Why are you adding voxels to the aparc+aseg in the insula? cheers Bruce On Wed, 29 Oct 2014, Adam Mezher wrote: > Hi Bruce and FS group, > Thanks again for the speedy replies and help with everything. Quick question > about editing voxels (specifically those in the lh/rh insula). Should I > simply add specific voxels to the aparc+aseg for this step? It was a little > unclear on the wiki. > > Also, is there a specific command to re-run the stats/etc. after these edits > are performed? > > Thanks a lot, > Adam > > ___ 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.
