Re: [Freesurfer] Hippocampus visualisation
That's super Eugenio, Thanks so much. Exactly what I needed. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 02 October 2015 10:57 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampus visualisation Hi Erik, one possible way of doing this: 1. For a single subfield: set the color map to Lookup Table. Tick "show as isosurface in 3d view". Tick "label volume". Then, set both values of the range to the numeric code of the subfield you want to display (e.g., for CA1, it would be 206). 2. For all subfields simultaneously: same as before, but setting the range to 200-226. This will color each subfield differently. 3. For showing the whole hippocampus in the same color: an easy, quick way is to switch the color map to grayscale, tick "show as isosurface in 3d view", untick "label volume", and set the lower and upper thresholds to 200 and 226, respectively. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Erik O'Hanlon" <erikohan...@rcsi.ie> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, October 2, 2015 10:31:17 AM Subject: [Freesurfer] Hippocampus visualisation Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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.
[Freesurfer] Hippocampus visualisation
Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] Hippocampus visualisation
Hi Erik, one possible way of doing this: 1. For a single subfield: set the color map to Lookup Table. Tick "show as isosurface in 3d view". Tick "label volume". Then, set both values of the range to the numeric code of the subfield you want to display (e.g., for CA1, it would be 206). 2. For all subfields simultaneously: same as before, but setting the range to 200-226. This will color each subfield differently. 3. For showing the whole hippocampus in the same color: an easy, quick way is to switch the color map to grayscale, tick "show as isosurface in 3d view", untick "label volume", and set the lower and upper thresholds to 200 and 226, respectively. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Erik O'Hanlon" <erikohan...@rcsi.ie> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, October 2, 2015 10:31:17 AM Subject: [Freesurfer] Hippocampus visualisation Hi Freesurfer experts, I've run the subfield analysis with Dev v6 and am just wondering if it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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.
