Re: [Freesurfer] Viewing vitamin E capsules?
Hi Seth do you really want to include the capsule within the brain mask? You can always view it and find its coordinate by visualizing the orig.mgz. If you really want it in the brainmask.mgz you can clone it back in using freeview or tkmedit cheers Bruce On Mon, 19 Oct 2015, Hutton, Seth wrote: Dear users, I have been using FreeSurfer for a while now, but am working in a new lab and their goals fall outside of my realm of experience. We are using both MRI imaging as well as FNIRs. We have multiple vitamin E capsules placed during both and would like to be able to view them in FreeSurfer so that we can better estimate the projected cortical localization of these capsules. Using the generic recon-all -s -i -all we are unable to see our capsules, as they are most likely eliminated during the skull strip step. I see that I can change the threshold with "-wsmore", but am wondering if this is really the best way to accomplish what we are trying to do. Is there any way to include our capsules without excluding the skull strip? If not could how would you recommend adjusting the threshold. I tried excluding the skulls trip step with recon-all -s -i -autorecon1 -noskullstrip but then when I tried to view it using free view it was unable to open due to the lack of the brain mask.mgz. Thank you so much for your time and consideration, Seth H ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ 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] Viewing vitamin E capsules?
Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there a more specific goal? hth d On 10/19/15 10:56 AM, Hutton, Seth wrote: > Dear users, > > I have been using FreeSurfer for a while now, but am working in a new > lab and their goals fall outside of my realm of experience. > We are using both MRI imaging as well as FNIRs. We have multiple vitamin > E capsules placed during both and would like to be able to view them in > FreeSurfer so that we can better estimate the projected cortical > localization of these capsules. > Using the generic recon-all -s -i -all we are unable to see our > capsules, as they are most likely eliminated during the skull strip > step. I see that I can change the threshold with "-wsmore", but am > wondering if this is really the best way to accomplish what we are > trying to do. > Is there any way to include our capsules without excluding the skull > strip? If not could how would you recommend adjusting the threshold. > I tried excluding the skulls trip step with > recon-all -s -i -autorecon1 -noskullstrip > but then when I tried to view it using free view it was unable to open > due to the lack of the brain mask.mgz. > > Thank you so much for your time and consideration, > Seth H > > ** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > > > > ___ > 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
[Freesurfer] Viewing vitamin E capsules?
Dear users, I have been using FreeSurfer for a while now, but am working in a new lab and their goals fall outside of my realm of experience. We are using both MRI imaging as well as FNIRs. We have multiple vitamin E capsules placed during both and would like to be able to view them in FreeSurfer so that we can better estimate the projected cortical localization of these capsules. Using the generic recon-all -s -i -all we are unable to see our capsules, as they are most likely eliminated during the skull strip step. I see that I can change the threshold with "-wsmore", but am wondering if this is really the best way to accomplish what we are trying to do. Is there any way to include our capsules without excluding the skull strip? If not could how would you recommend adjusting the threshold. I tried excluding the skulls trip step with recon-all -s -i -autorecon1 -noskullstrip but then when I tried to view it using free view it was unable to open due to the lack of the brain mask.mgz. Thank you so much for your time and consideration, Seth H ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ 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.
