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 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> : > 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-bounces@ > 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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas > Fernández <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>: > > 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 > 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. 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