Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ 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. 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.
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ 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. 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.
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ 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. 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.
Hi Ed,
sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization.
cheers Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ 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. 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.
Hi Bruce,
It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions.
Cheers, Ed
On 10 Jul 2012, at 16:57, Bruce Fischl wrote:
Hi Ed,
sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization.
cheers Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi,
I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap).
The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows:
bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3
and inspected the result with
tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf
The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1.
It makes hardly any difference if instead of --t1 --t2 as contrast setting was used.
Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR?
(FreeSurfer v4.5.0, MacOSX 10.5)
Cheers, Ed _______________________________________________ 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. 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.
glad to hear it :). You may need to repost (and possibly upload your data) On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions.
Cheers, Ed
On 10 Jul 2012, at 16:57, Bruce Fischl wrote:
Hi Ed,
sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization.
cheers Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
try -init-spm
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
> Hi, > > I would like to register FLAIR to T1. > Specifications FLAIR: > axial acquisition, 24 slices, > pixel size = 0.45 * 0.45 mm^2 > slice thickness = 5.50 mm (no gap). > > The slices run from the top of the brain > to just below the eyes. This is contrary > to the T1 scan which covers the full head > down to the neck. > I have tried bbregiser as follows: > > bbregister --s 001 --mov 001_FLAIR.mgz \ > --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 > > and inspected the result with > > tkregister2 --mov 001_FLAIR.mgz \ > --reg 001_register.dat --surf > > The result looks bad, it is displaced and rotated > by about 20 degrees with respect to T1. > > It makes hardly any difference if instead of --t1 > --t2 as contrast setting was used. > > Is there a better way to do this registration? > For instance, should I crop T1 to about the > same space as covered by FLAIR? > > (FreeSurfer v4.5.0, MacOSX 10.5) > > Cheers, > Ed > _______________________________________________ > 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. 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.
Often with FLAIR there is not enough gray-white contrast to run the registration. Try using the pial surface instead, with "-surf pial --t1" This tells it to use the pial surface as a boundary. The --t1 is needed because the intensity should go from bright to dark. Let me know if that does not fix the problem. doug
On 07/10/2012 11:58 AM, Bruce Fischl wrote:
glad to hear it :). You may need to repost (and possibly upload your data) On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is indeed from the same scan session. I'll wait patiently, let Doug enjoy his vacation before he gets bothered again by all our questions.
Cheers, Ed
On 10 Jul 2012, at 16:57, Bruce Fischl wrote:
Hi Ed,
sorry, you'll have to wait until Doug is back from vacation. Is this from the same session? I've always had it work on flair images using one of the types of initialization.
cheers Bruce
On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
Unfortunately, this has no effect.
Ed
On 10 Jul 2012, at 16:40, Bruce Fischl wrote:
Hi Ed
you are using -t2, right? You can also try -init-header
cheers Bruce On Tue, 10 Jul 2012, Ed Gronenschild wrote:
Hi Bruce,
It is slightly better but still displacements in all directions and rotations too exist.
Ed
On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
> try -init-spm > > cheers > Bruce > On Tue, 10 Jul 2012, Ed Gronenschild wrote: > >> Hi, >> >> I would like to register FLAIR to T1. >> Specifications FLAIR: >> axial acquisition, 24 slices, >> pixel size = 0.45 * 0.45 mm^2 >> slice thickness = 5.50 mm (no gap). >> >> The slices run from the top of the brain >> to just below the eyes. This is contrary >> to the T1 scan which covers the full head >> down to the neck. >> I have tried bbregiser as follows: >> >> bbregister --s 001 --mov 001_FLAIR.mgz \ >> --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 >> >> and inspected the result with >> >> tkregister2 --mov 001_FLAIR.mgz \ >> --reg 001_register.dat --surf >> >> The result looks bad, it is displaced and rotated >> by about 20 degrees with respect to T1. >> >> It makes hardly any difference if instead of --t1 >> --t2 as contrast setting was used. >> >> Is there a better way to do this registration? >> For instance, should I crop T1 to about the >> same space as covered by FLAIR? >> >> (FreeSurfer v4.5.0, MacOSX 10.5) >> >> Cheers, >> Ed >> _______________________________________________ >> 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. 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. >
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