Copy the lta to subject/mri/transforms/FLAIRraw.lta (there should be one there already, just copy over it)


On 4/16/2021 12:19 PM, Edina Szabó wrote:
> > External Email - Use Caution > > Hi Douglas, > > Thank you for your response! I really appreciate it. > > I ran the command – it works if I replace --i with --mov. > > How can I use the new FLAIRraw.lta to create a new FLAIR-based pial > surface? For example, should I run recon-all -autorecon2 or some > later step? > > Also, we were assuming that registration of the FLAIR to the T1 was > the problem (underestimated pial surface), since the FLAIR.mgz > produced by Freesurfer was not well registered to the T1.mgz. So, if > that's the case, and I have another well-registered FLAIR (using FSL > or SPM), is there a way to skip the Freesurfer registration and use > that FLAIR to create the FLAIR pial surface? > > Thank you for your help in advance! > > All the best, Edina Szabo > > __ Edina Szabo, PhD Research Fellow Department of Anesthesiology, > Critical Care and Pain Medicine Boston Children's Hospital | Harvard > Medical School > > ----------------- > > Try this cd subject/mri mri_coreg --i orig/T2raw.mgz --targ orig.mgz > --reg transforms/T2raw.lta You can run with multiple threads by > adding --threads N where N is the number of threads On 3/29/2021 5:18 > PM, Edina Szabó wrote: > > External Email - Use Caution > > Dear All, > > We are running recon-all on the latest version of FreeSurfer > (v7.1.1). We are using both T1 and FLAIR images to better define the > pial surfaces, but when we run the recommended command line > (recon-all -subject subjectname -i /path/to/input_volume -FLAIR > /path/to/FLAIR_volume -FLAIRpial -all) the pial surface is very > underestimated (?.pial.FLAIR – and the aseg volume is based on these > surfaces), and we get better results without the FLAIR. It seems that > FreeSurfer mis-registers the FLAIR to the T1 during the process. Is > there a separate step we should do to register FLAIR to T1? > > Thank you, Edina > > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://secure-web.cisco.com/1MJbXPp3_g04XOv4-n3hWV1ItlnkWJJXvDaY0EbvfBTvIHv0zKVVk-G9L4Ajg7-U6fy7EQJQiG11RZUTUpm3kuhHg3ZUCd4Hnm66L-fgt_mdgM4sPUrAIdVBc6pqDy0ZYn4kGyvYevBBGjj-p4NSypd99OfO0ddNrGa1znR0My1Byl4BuSOkN2S2yxkt25b5vobQL3K5cgzx25iT4rg24j4QKadAy9hpngO0Pbte5tMLamzLoEED0J6X0axUHf4c-y5amdYCRzFT8UQ3dqtnO1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________
> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://secure-web.cisco.com/1MJbXPp3_g04XOv4-n3hWV1ItlnkWJJXvDaY0EbvfBTvIHv0zKVVk-G9L4Ajg7-U6fy7EQJQiG11RZUTUpm3kuhHg3ZUCd4Hnm66L-fgt_mdgM4sPUrAIdVBc6pqDy0ZYn4kGyvYevBBGjj-p4NSypd99OfO0ddNrGa1znR0My1Byl4BuSOkN2S2yxkt25b5vobQL3K5cgzx25iT4rg24j4QKadAy9hpngO0Pbte5tMLamzLoEED0J6X0axUHf4c-y5amdYCRzFT8UQ3dqtnO1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________
> Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
t