Re: [Freesurfer] ?Sequence for Hippo_subfields
Hi Kev, 1. It will able to use only the T1, only the T2, or both simultaneously. 2. The algorithm is relatively robust against these parameters. However, the higher the resolution and the lower the noise the better (as usual). 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 - Original Message - From: Schumman schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 16, 2014 6:47:21 PM Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Dear Eugenio, I'm following up on this thread. After some discussion with the radiologist, some relevant questions have come up: 1. Is Freesurfer going to make use of both the T1 and the T2 sequences in the processing stream of hippocampal subfields? 2. If the answer is yes how important is that the T1 weighted and the T2 sequences are similar in terms on slice thickness (eg. both 1mm ISO), FOV, and other parameters? Thanks, Kev On 2014-06-12, at 12:36 PM, Eugenio Iglesias wrote: Yes! If Im not mistaken, ADNI is acquiring this type of data on 3T platforms. 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 - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST) Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ?Sequence for Hippo_subfields
Dear Eugenio, I'm following up on this thread. After some discussion with the radiologist, some relevant questions have come up: 1. Is Freesurfer going to make use of both the T1 and the T2 sequences in the processing stream of hippocampal subfields? 2. If the answer is yes how important is that the T1 weighted and the T2 sequences are similar in terms on slice thickness (eg. both 1mm ISO), FOV, and other parameters? Thanks, Kev On 2014-06-12, at 12:36 PM, Eugenio Iglesias wrote: Yes! If Im not mistaken, ADNI is acquiring this type of data on 3T platforms. 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 - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST) Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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 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
Re: [Freesurfer] ?Sequence for Hippo_subfields
Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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
Re: [Freesurfer] ?Sequence for Hippo_subfields
Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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 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] ?Sequence for Hippo_subfields
Yes! If Im not mistaken, ADNI is acquiring this type of data on 3T platforms. 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 - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST) Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [Freesurfer] ?Sequence for Hippo_subfields Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ?Sequence for Hippo_subfields
Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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.
