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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
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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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Edina Szabó