External Email - Use Caution Sorry if I didn’t explain myself properly. T2 scans of the whole head can be used by recon-all to improve the segmentation of the pial surface, but: a) They are not required (you can use the T1 alone); and b) Cannot be run through recon-all independently from the T1. For hippocampal subfields: the T2 scan is used in a separate stream. In fact, their field of view doesn’t even have to cover the whole head – just the hippocampi (this is what the ADNI highres T2 protocol does). Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of M Janani <janan...@hcl.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, 4 May 2018 at 08:26 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command External Email - Use Caution Thanks for your reply Eugenio. You have mentioned like “No recon-all on the T2 required, as it's used in a different way”. May I know the actual purpose of using T2 images for reconstruction process. Why we should not T2 images as input for recon-all command. Regards, Janani From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: 04 May 2018 12:50 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command External Email - Use Caution Hola Miguel Ángel, First, you need to run the T1 through recon-all normally, as you have already done. Next, you run the subfield module with the highres T2 as input - no recon-all on the T2 required, as it's used in a different way. Cheers Eugenio Sent from my phone, please excuse brevity and typos ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Miguel Ángel Rivas Fernández <miguelrivasf...@gmail.com<mailto:miguelrivasf...@gmail.com>> Sent: Thursday, May 3, 2018 11:08:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command External Email - Use Caution Hi Freesurfer developers, I have executed the recon-all command using the T1 images but I would be interested in doing a reconstruction of the hippocampal subregions using for that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields<https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields&data=02%7C01%7Cjananimj%40hcl.com%7C733fab39e9994ea213fb08d5b18f8582%7C189de737c93a4f5a8b686f4ca9941912%7C0%7C1%7C636610152364530300&sdata=H1MJaa6TKp%2BOBlGtJM%2F%2BjnQBIdhAWvUS94hG9a3kC8c%3D&reserved=0> that is possible make hippocampal segmentation using the T2 images, but if T2 images cannot be used as input to execute the recon-all in consecuence I can´t do the segmentation of hippocampal subfields or on the contrary the recon-all and the hippocampal subfields segmentation are two operations that can be executed independently ? I hope to have explained myself correctly Thanks in advance. Cheers 2018-05-03 18:28 GMT+02:00 Douglas N. Greve <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>: No, not currently On 05/03/2018 11:26 AM, M Janani wrote: > > Hi Team, > > I have one doubt. Can I input T2 weighted images for > recon-all command? > > Regards, > > Janani > > ::DISCLAIMER:: > -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > The contents of this e-mail and any attachment(s) are confidential and > intended for the named recipient(s) only. E-mail transmission is not > guaranteed to be secure or error-free as information could be > intercepted, corrupted, lost, destroyed, arrive late or incomplete, or > may contain viruses in transmission. The e mail and its contents (with > or without referred errors) shall therefore not attach any liability > on the originator or HCL or its affiliates. Views or opinions, if any, > presented in this email are solely those of the author and may not > necessarily reflect the views or opinions of HCL or its affiliates. > Any form of reproduction, dissemination, copying, disclosure, > modification, distribution and / or publication of this message > without the prior written consent of authorized representative of HCL > is strictly prohibited. If you have received this email in error > please delete it and notify the sender immediately. Before opening any > email and/or attachments, please check them for viruses and other defects. > -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cjananimj%40hcl.com%7C733fab39e9994ea213fb08d5b18f8582%7C189de737c93a4f5a8b686f4ca9941912%7C0%7C1%7C636610152364530300&sdata=V0XZLuCREOdisgrO5ARWU7fwIFlHHRf4RHdccsdVbY4%3D&reserved=0> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cjananimj%40hcl.com%7C733fab39e9994ea213fb08d5b18f8582%7C189de737c93a4f5a8b686f4ca9941912%7C0%7C1%7C636610152364530300&sdata=V0XZLuCREOdisgrO5ARWU7fwIFlHHRf4RHdccsdVbY4%3D&reserved=0> 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<https://apac01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=02%7C01%7Cjananimj%40hcl.com%7C733fab39e9994ea213fb08d5b18f8582%7C189de737c93a4f5a8b686f4ca9941912%7C0%7C1%7C636610152364530300&sdata=JegvW8pYxJS2hFrwq51v6CTy%2BRaCrgXLS31VRVxVwx0%3D&reserved=0> . 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. -- Miguel Ángel Rivas Fernández
_______________________________________________ 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.
