I wonder whether there is a way to convert surfaces back to the subject native space. Thanks!
Anqi Qiu Center for Imaging Science The Johns Hopkins University
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: Tuesday, February 06, 2007 11:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 36, Issue 10
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Today's Topics:
1. Re: tkregister2:views mixed up. (Chacko Cherian) 2. Re: tkregister2:views mixed up. (Doug Greve) 3. Re: brainmask.mgz problems (Bruce Fischl) 4. error with mri_ca_register (Binyam Nardos)
----------------------------------------------------------------------
Message: 1 Date: Mon, 5 Feb 2007 15:47:55 -0800 (PST) From: Chacko Cherian chacko_cherian@yahoo.com Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Doug Greve greve@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: 570151.930.qm@web35315.mail.mud.yahoo.com Content-Type: text/plain; charset=iso-8859-1
Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm?
Thanks a lot!
Chacko. --- Doug Greve greve@nmr.mgh.harvard.edu wrote:
I mean to just load the orig.mgz into tkmedit and see if it is oriented correctly. Assuming that it is oriented correctly, then it sounds like the talairach transform is messed up pretty badly. When you run tkregister2, try adding --regheader. This will ignore the info in the talairaach.xfm file and force it to use the geometry info. it will likely be very far off, but the basic orientation should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the transform..i checked brainmask.img and T1.img after loading the transform and they had this
problem..The
header and geometry info look fine..
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
That means that the geometry info in the file is messed up. Where did the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
Hello ALL,
Has anybody had trouble with tkregister2..I
loaded
the
transform and the coronal and horizontal views
are
mixed up.Coronal view of the subject is coupled
with
the horizontal view of the talairach volume.
Thanks in advance Regards,
Chacko.
TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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------------------------------
Message: 2 Date: Mon, 05 Feb 2007 20:20:04 -0500 From: Doug Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Chacko Cherian chacko_cherian@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: 45C7D7C4.2070908@nmr.mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
You can start with that one and fix it by hand (which is a hassle). We are working on ways to make the talairach more robust. BTW, if you run tkregister2 again after fixing it, you should not include the --regheader as that will ignore your previous edits.
doug
Chacko Cherian wrote:
Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm?
Thanks a lot!
Chacko. --- Doug Greve greve@nmr.mgh.harvard.edu wrote:
I mean to just load the orig.mgz into tkmedit and see if it is oriented correctly. Assuming that it is oriented correctly, then it sounds like the talairach transform is messed up pretty badly. When you run tkregister2, try adding --regheader. This will ignore the info in the talairaach.xfm file and force it to use the geometry info. it will likely be very far off, but the basic orientation should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the transform..i checked brainmask.img and T1.img after loading the transform and they had this
problem..The
header and geometry info look fine..
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
That means that the geometry info in the file is messed up. Where did the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
>Hello ALL, > >Has anybody had trouble with tkregister2..I > > > >
loaded
> > > > > > the
>transform and the coronal and horizontal views > > > >
are
>mixed up.Coronal view of the subject is coupled > > > > > > with
>the horizontal view of the talairach volume. > >Thanks in advance >Regards, > >Chacko. > > > > > > > > >
>TV dinner still cooling? >Check out "Tonight's Picks" on Yahoo! TV. >http://tv.yahoo.com/ >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail
arrives.
http://tools.search.yahoo.com/toolbar/features/mail/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Never miss an email again!
=== message truncated ===
Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and
hotel bargains.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
You can create a binary mask with mri_surf2vol
anqi wrote:
I wonder whether there is a way to convert surfaces back to the subject native space. Thanks!
Anqi Qiu Center for Imaging Science The Johns Hopkins University
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: Tuesday, February 06, 2007 11:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 36, Issue 10
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: tkregister2:views mixed up. (Chacko Cherian)
- Re: tkregister2:views mixed up. (Doug Greve)
- Re: brainmask.mgz problems (Bruce Fischl)
- error with mri_ca_register (Binyam Nardos)
Message: 1 Date: Mon, 5 Feb 2007 15:47:55 -0800 (PST) From: Chacko Cherian chacko_cherian@yahoo.com Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Doug Greve greve@nmr.mgh.harvard.edu Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: 570151.930.qm@web35315.mail.mud.yahoo.com Content-Type: text/plain; charset=iso-8859-1
Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm?
Thanks a lot!
Chacko. --- Doug Greve greve@nmr.mgh.harvard.edu wrote:
I mean to just load the orig.mgz into tkmedit and see if it is oriented correctly. Assuming that it is oriented correctly, then it sounds like the talairach transform is messed up pretty badly. When you run tkregister2, try adding --regheader. This will ignore the info in the talairaach.xfm file and force it to use the geometry info. it will likely be very far off, but the basic orientation should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the transform..i checked brainmask.img and T1.img after loading the transform and they had this
problem..The
header and geometry info look fine..
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
That means that the geometry info in the file is messed up. Where did the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Does it view correctly in tkmedit?
Chacko Cherian wrote:
>Hello ALL, > >Has anybody had trouble with tkregister2..I > > > >
loaded
> > > > > > the
>transform and the coronal and horizontal views > > > >
are
>mixed up.Coronal view of the subject is coupled > > > > > > with
>the horizontal view of the talairach volume. > >Thanks in advance >Regards, > >Chacko. > > > > > > > > >
>TV dinner still cooling? >Check out "Tonight's Picks" on Yahoo! TV. >http://tv.yahoo.com/ >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail
arrives.
http://tools.search.yahoo.com/toolbar/features/mail/
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Never miss an email again!
=== message truncated ===
Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097
Message: 2 Date: Mon, 05 Feb 2007 20:20:04 -0500 From: Doug Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkregister2:views mixed up. To: Chacko Cherian chacko_cherian@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Message-ID: 45C7D7C4.2070908@nmr.mgh.harvard.edu Content-Type: text/plain; charset="us-ascii"
You can start with that one and fix it by hand (which is a hassle). We are working on ways to make the talairach more robust. BTW, if you run tkregister2 again after fixing it, you should not include the --regheader as that will ignore your previous edits.
doug
Chacko Cherian wrote:
Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm?
Thanks a lot!
Chacko. --- Doug Greve greve@nmr.mgh.harvard.edu wrote:
I mean to just load the orig.mgz into tkmedit and see if it is oriented correctly. Assuming that it is oriented correctly, then it sounds like the talairach transform is messed up pretty badly. When you run tkregister2, try adding --regheader. This will ignore the info in the talairaach.xfm file and force it to use the geometry info. it will likely be very far off, but the basic orientation should be ok.
Chacko Cherian wrote:
It has the problem in tkmedit,after I load the transform..i checked brainmask.img and T1.img after loading the transform and they had this
problem..The
header and geometry info look fine..
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
That means that the geometry info in the file is messed up. Where did the data come from? Are the dicoms messed up too?
Chacko Cherian wrote:
No, It has the same problem in tkmedit too.
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
>Does it view correctly in tkmedit? > >Chacko Cherian wrote: > > > > > > > > > >>Hello ALL, >> >>Has anybody had trouble with tkregister2..I >> >> >> >> >> >>
loaded
>> >> >> >> >> >> >> >> >the > > > > > > > > >>transform and the coronal and horizontal views >> >> >> >> >> >>
are
>>mixed up.Coronal view of the subject is coupled >> >> >> >> >> >> >> >> >with > > > > > > > > >>the horizontal view of the talairach volume. >> >>Thanks in advance >>Regards, >> >>Chacko. >> >> >> >> >> >> >> >> >> >> >>
> > > > > > > > >>TV dinner still cooling? >>Check out "Tonight's Picks" on Yahoo! TV. >>http://tv.yahoo.com/ >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer@nmr.mgh.harvard.edu >> >> >> >> >> >> >> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > > > > > >> >> >> >> >> >> >> >> >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve@nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >In order to help us help you, please follow the steps in: >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu > > > > > > > > >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail
arrives.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Never miss an email again!
=== message truncated ===
Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and
hotel bargains.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
anqi -
Doug Greve