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 > >
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