External Email - Use Caution It depends on the version, but yes, in 6.0 it’d be that command. The file name of the additional scan should be an existing nii/nii.gz/mgz file, though (right now you just have “T2”). Cheers, /E
-- 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 Miguel Ángel Rivas Fernández <miguelrivasf...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, 4 May 2018 at 09:46 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 Hi, What would be the command for hippocampal subfields using only the T2 images? This? recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID> I tried but obtained the following error pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2 -hippocampal-subfields-T2 T2 T2_3D_SAG ERROR: cannot find T2 Darwin pcpb3846.inv.usc.es<http://pcpb3846.inv.usc.es> 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan 30 11:45:51 PST 2018; root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64 recon-all -s 4235_T2 exited with ERRORS at Fri May 4 10:43:04 CEST 2018 Thanks cheers, 2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>: 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of M Janani <janan...@hcl.com<mailto:janan...@hcl.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, 4 May 2018 at 08:26 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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> [mailto: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<mailto:freesurfer@nmr.mgh.harvard.edu>>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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. 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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<mailto: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. -- Miguel Ángel Rivas Fernández
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